https://bioinformaticsonline.com/snippets?offset=220 https://bioinformaticsonline.com/snippets/view/41931/extract-the-sequence-by-ids Fri, 03 Jul 2020 04:58:39 -0500 https://bioinformaticsonline.com/snippets/view/41931/extract-the-sequence-by-ids #This method can be applied directly to FASTA or a FASTQ file, compressed or uncompressed files. Seqtk is a fast and lightweight tool for processing biological data (FASTA/FASTQ). if you have a list of identifiers that you would like to extract from a file, you can run this command as follows: #Extract sequences with names in file name.list, one sequence name per line: seqtk subseq input.fasta name.list > output.fasta]]> Surabhi Chaudhary https://bioinformaticsonline.com/snippets/view/41724/copy-files-fromto-docker Tue, 26 May 2020 07:38:40 -0500 https://bioinformaticsonline.com/snippets/view/41724/copy-files-fromto-docker #Find out a container’s name or ID using the docker ps command: $ docker ps CONTAINER ID IMAGE COMMAND CREATED STATUS PORTS NAMES 72ca2488b353 my_image X hours ago Up X hours my_container #Copy a file from host to container: $ docker cp foo.txt 72ca2488b353:/foo.txt #Copy a file from Docker container to host: $ docker cp 72ca2488b353:/foo.txt foo.txt]]> Jit https://bioinformaticsonline.com/snippets/view/41712/setting-up-autocontampr Sun, 24 May 2020 10:03:31 -0500 https://bioinformaticsonline.com/snippets/view/41712/setting-up-autocontampr (base) jit@jit-HP-Pro-3335-MT:~/Downloads/testDock$ docker build -t autocontampr . Sending build context to Docker daemon 9.024MB Step 1/16 : FROM ubuntu:14.04 ---> 6e4f1fe62ff1 Step 2/16 : FROM perl:latest ---> de6996f7ef50 Step 3/16 : FROM bioperl/bioperl-deps ---> e890cc223da3 Step 4/16 : MAINTAINER "Jitendra Narayan" <jnarayan81@gmail.com> ---> Using cache ---> c0e65f263890 Step 5/16 : RUN apt-get clean && apt-get update --yes && apt-get install --yes git && apt-get install -y wget ---> Using cache ---> 646453255081 Step 6/16 : RUN apt-get install --yes build-essential gcc-multilib perl ---> Using cache ---> 5c8f91f5e722 Step 7/16 : RUN apt-get -y install r-base ---> Using cache ---> e2f4b21b0c27 Step 8/16 : RUN echo "r <- getOption('repos'); r['CRAN'] <- 'http://cran.us.r-project.org'; options(repos = r);" > ~/.Rprofile ---> Using cache ---> 113232f4f250 Step 9/16 : RUN Rscript -e "install.packages('ggplot2')" ---> Using cache ---> 0953f592efa6 Step 10/16 : RUN wget http://www.zlib.net/zlib-1.2.11.tar.gz && tar -xzf zlib-1.2.11.tar.gz && cd zlib-1.2.11 && ./configure && make && sudo make install && cd .. ---> Using cache ---> 850cb02378d4 Step 11/16 : RUN wget https://sourceforge.net/projects/staden/files/io_lib/1.9.0/io_lib-1.9.0.tar.gz && tar -xzf io_lib-1.9.0.tar.gz && cd io_lib-1.9.0 && export CFLAGS="-fPIC" && ./configure && make && sudo make install && cd .. ---> Using cache ---> 1acadedd1157 Step 12/16 : RUN apt-get install -y bioperl && apt-get install -y libstatistics-distributions-perl && apt-get install -y libterm-progressbar-simple-perl && apt-get install -y libbio-scf-perl ---> Running in 7adc9dbdb955 Reading package lists... Building dependency tree... Reading state information... The following extra packages will be installed: amap-align apache2-bin bedtools bioperl-run blast2 bowtie bwa clustalw dialign emboss emboss-data emboss-lib exonerate ghostscript gsfonts hmmer infernal kalign libace-perl libalgorithm-c3-perl libalgorithm-munkres-perl libapache-dbi-perl libapache2-mod-perl2 libapache2-reload-perl libapr1 libaprutil1 libaprutil1-dbd-sqlite3 libaprutil1-ldap libarray-compare-perl libavahi-client3 libavahi-common-data libavahi-common3 libb-hooks-endofscope-perl libbio-asn1-entrezgene-perl libbio-perl-perl libbio-perl-run-perl libbit-vector-perl libbsd-resource-perl libcache-cache-perl libcarp-clan-perl libclass-c3-perl libclass-c3-xs-perl libclass-inspector-perl libclass-load-perl libclass-load-xs-perl libclass-tiny-perl libclone-perl libconvert-binary-c-perl libconvert-binhex-perl libcrypt-ssleay-perl libcups2 libcupsfilters1 libcupsimage2 libdata-optlist-perl libdata-stag-perl libdate-calc-perl libdate-calc-xs-perl libdate-manip-perl libdevel-caller-perl libdevel-globaldestruction-perl libdevel-lexalias-perl libdevel-partialdump-perl libdevel-symdump-perl libeval-closure-perl libfcgi-perl libfile-slurp-perl libfreezethaw-perl libgd-gd2-perl libgraph-perl libgraphviz-perl libgs9 libgs9-common libheap-perl libhpdf-2.2.1 libhtml-tableextract-perl libijs-0.35 libio-pty-perl libio-sessiondata-perl libio-string-perl libio-stringy-perl libipc-run-perl libipc-sharelite-perl libjbig2dec0 libjcode-pm-perl libmath-derivative-perl libmath-spline-perl libmime-tools-perl libmldbm-perl libmodule-implementation-perl libmodule-runtime-perl libmoose-perl libmro-compat-perl libnamespace-clean-perl libncbi6 libole-storage-lite-perl libossp-uuid-perl libossp-uuid16 libpackage-deprecationmanager-perl libpackage-stash-perl libpackage-stash-xs-perl libpadwalker-perl libparams-classify-perl libparams-util-perl libparse-recdescent-perl libperl5.18 libpostscript-perl libruby1.9.1 libset-scalar-perl libsoap-lite-perl libsort-naturally-perl libspreadsheet-parseexcel-perl libspreadsheet-writeexcel-perl libstatistics-descriptive-perl libsub-exporter-perl libsub-exporter-progressive-perl libsub-identify-perl libsub-install-perl libsub-name-perl libsvg-graph-perl libsvg-perl libtask-weaken-perl libtie-ixhash-perl libtree-dagnode-perl libtry-tiny-perl libunicode-map-perl libvariable-magic-perl libxml-dom-perl libxml-dom-xpath-perl libxml-filter-buffertext-perl libxml-libxml-perl libxml-libxslt-perl libxml-namespacesupport-perl libxml-perl libxml-regexp-perl libxml-sax-base-perl libxml-sax-expat-perl libxml-sax-perl libxml-sax-writer-perl libxml-simple-perl libxml-twig-perl libxml-writer-perl libxml-xpath-perl libxml-xpathengine-perl libxmlrpc-lite-perl libyaml-0-2 libyaml-libyaml-perl libyaml-perl lynx lynx-cur mafft maq muscle ncbi-data perl-doc perl-tk phyml poppler-data primer3 probalign probcons ruby ruby1.9.1 samtools sim4 t-coffee tigr-glimmer tm-align wise wise-data Suggested packages: www-browser apache2-doc apache2-suexec-pristine apache2-suexec-custom filo gmap paml phylip libvibrant6b ncbi-rrna-data ncbi-tools-bin ncbi-tools-x11 bowtie-examples clustalx seaview emboss-doc emboss-test embassy ghostscript-x hpijs hmmer-doc libxml-sax-expatxs-perl cups-common fonts-droid libhtml-element-extended-perl uuid libscalar-number-perl libmime-lite-perl libnet-jabber-perl libunicode-map8-perl libunicode-string-perl xml-twig-tools libyaml-shell-perl groff poppler-utils fonts-japanese-mincho fonts-ipafont-mincho fonts-japanese-gothic fonts-ipafont-gothic fonts-arphic-ukai fonts-arphic-uming fonts-unfonts-core ncbi-epcr probcons-extra ri ruby-dev ruby1.9.1-examples ri1.9.1 ruby1.9.1-dev ruby-switch boxshade t-coffee-examples dialign-tx poa proda pymol rasmol wise-doc Recommended packages: libgd-perl The following NEW packages will be installed: amap-align apache2-bin bedtools bioperl bioperl-run blast2 bowtie bwa clustalw dialign emboss emboss-data emboss-lib exonerate ghostscript gsfonts hmmer infernal kalign libace-perl libalgorithm-c3-perl libalgorithm-munkres-perl libapache-dbi-perl libapache2-mod-perl2 libapache2-reload-perl libapr1 libaprutil1 libaprutil1-dbd-sqlite3 libaprutil1-ldap libarray-compare-perl libavahi-client3 libavahi-common-data libavahi-common3 libb-hooks-endofscope-perl libbio-asn1-entrezgene-perl libbio-perl-perl libbio-perl-run-perl libbit-vector-perl libbsd-resource-perl libcache-cache-perl libcarp-clan-perl libclass-c3-perl libclass-c3-xs-perl libclass-inspector-perl libclass-load-perl libclass-load-xs-perl libclass-tiny-perl libclone-perl libconvert-binary-c-perl libconvert-binhex-perl libcrypt-ssleay-perl libcups2 libcupsfilters1 libcupsimage2 libdata-optlist-perl libdata-stag-perl libdate-calc-perl libdate-calc-xs-perl libdate-manip-perl libdevel-caller-perl libdevel-globaldestruction-perl libdevel-lexalias-perl libdevel-partialdump-perl libdevel-symdump-perl libeval-closure-perl libfcgi-perl libfile-slurp-perl libfreezethaw-perl libgd-gd2-perl libgraph-perl libgraphviz-perl libgs9 libgs9-common libheap-perl libhpdf-2.2.1 libhtml-tableextract-perl libijs-0.35 libio-pty-perl libio-sessiondata-perl libio-string-perl libio-stringy-perl libipc-run-perl libipc-sharelite-perl libjbig2dec0 libjcode-pm-perl libmath-derivative-perl libmath-spline-perl libmime-tools-perl libmldbm-perl libmodule-implementation-perl libmodule-runtime-perl libmoose-perl libmro-compat-perl libnamespace-clean-perl libncbi6 libole-storage-lite-perl libossp-uuid-perl libossp-uuid16 libpackage-deprecationmanager-perl libpackage-stash-perl libpackage-stash-xs-perl libpadwalker-perl libparams-classify-perl libparams-util-perl libparse-recdescent-perl libperl5.18 libpostscript-perl libruby1.9.1 libset-scalar-perl libsoap-lite-perl libsort-naturally-perl libspreadsheet-parseexcel-perl libspreadsheet-writeexcel-perl libstatistics-descriptive-perl libsub-exporter-perl libsub-exporter-progressive-perl libsub-identify-perl libsub-install-perl libsub-name-perl libsvg-graph-perl libsvg-perl libtask-weaken-perl libtie-ixhash-perl libtree-dagnode-perl libtry-tiny-perl libunicode-map-perl libvariable-magic-perl libxml-dom-perl libxml-dom-xpath-perl libxml-filter-buffertext-perl libxml-libxml-perl libxml-libxslt-perl libxml-namespacesupport-perl libxml-perl libxml-regexp-perl libxml-sax-base-perl libxml-sax-expat-perl libxml-sax-perl libxml-sax-writer-perl libxml-simple-perl libxml-twig-perl libxml-writer-perl libxml-xpath-perl libxml-xpathengine-perl libxmlrpc-lite-perl libyaml-0-2 libyaml-libyaml-perl libyaml-perl lynx lynx-cur mafft maq muscle ncbi-data perl-doc perl-tk phyml poppler-data primer3 probalign probcons ruby ruby1.9.1 samtools sim4 t-coffee tigr-glimmer tm-align wise wise-data 0 upgraded, 170 newly installed, 0 to remove and 50 not upgraded. Need to get 134 MB of archives. After this operation, 749 MB of additional disk space will be used. Get:1 http://archive.ubuntu.com/ubuntu/ trusty/main libapr1 amd64 1.5.0-1 [85.1 kB] Get:2 http://archive.ubuntu.com/ubuntu/ trusty/main libaprutil1 amd64 1.5.3-1 [76.4 kB] Get:3 http://archive.ubuntu.com/ubuntu/ trusty-updates/main libavahi-common-data amd64 0.6.31-4ubuntu1.3 [21.1 kB] Get:4 http://archive.ubuntu.com/ubuntu/ trusty-updates/main libavahi-common3 amd64 0.6.31-4ubuntu1.3 [21.7 kB] Get:5 http://archive.ubuntu.com/ubuntu/ trusty-updates/main libavahi-client3 amd64 0.6.31-4ubuntu1.3 [25.2 kB] Get:6 http://archive.ubuntu.com/ubuntu/ trusty-updates/main libcups2 amd64 1.7.2-0ubuntu1.11 [178 kB] Get:7 http://archive.ubuntu.com/ubuntu/ trusty-updates/main libcupsfilters1 amd64 1.0.52-0ubuntu1.8 [73.7 kB] Get:8 http://archive.ubuntu.com/ubuntu/ trusty-updates/main libcupsimage2 amd64 1.7.2-0ubuntu1.11 [15.4 kB] Get:9 http://archive.ubuntu.com/ubuntu/ trusty/universe ncbi-data all 6.1.20120620-7 [5863 kB] Get:10 http://archive.ubuntu.com/ubuntu/ trusty/universe libncbi6 amd64 6.1.20120620-7 [4725 kB] Get:11 http://archive.ubuntu.com/ubuntu/ trusty-updates/main libyaml-0-2 amd64 0.1.4-3ubuntu3.1 [48.1 kB] Get:12 http://archive.ubuntu.com/ubuntu/ trusty/main poppler-data all 0.4.6-4 [1479 kB] Get:13 http://archive.ubuntu.com/ubuntu/ trusty/universe wise-data all 2.4.1-14 [33.9 kB] Get:14 http://archive.ubuntu.com/ubuntu/ trusty/universe wise amd64 2.4.1-14 [951 kB] Get:15 http://archive.ubuntu.com/ubuntu/ trusty/universe amap-align amd64 2.2-4 [158 kB] Get:16 http://archive.ubuntu.com/ubuntu/ trusty/main libaprutil1-dbd-sqlite3 amd64 1.5.3-1 [10.5 kB] Get:17 http://archive.ubuntu.com/ubuntu/ trusty/main libaprutil1-ldap amd64 1.5.3-1 [8634 B] Get:18 http://archive.ubuntu.com/ubuntu/ trusty-updates/main apache2-bin amd64 2.4.7-1ubuntu4.22 [845 kB] Get:19 http://archive.ubuntu.com/ubuntu/ trusty/universe bedtools amd64 2.17.0-1 [431 kB] Get:20 http://archive.ubuntu.com/ubuntu/ trusty/main libio-string-perl all 1.08-3 [11.1 kB] Get:21 http://archive.ubuntu.com/ubuntu/ trusty/universe libdata-stag-perl all 0.13-1 [429 kB] Get:22 http://archive.ubuntu.com/ubuntu/ trusty/universe libbio-perl-perl all 1.6.923-1 [4732 kB] Get:23 http://archive.ubuntu.com/ubuntu/ trusty/universe bioperl all 1.6.923-1 [386 kB] Get:24 http://archive.ubuntu.com/ubuntu/ trusty/universe libbio-perl-run-perl all 1.6.9-2 [897 kB] Get:25 http://archive.ubuntu.com/ubuntu/ trusty/universe bioperl-run all 1.6.9-2 [42.0 kB] Get:26 http://archive.ubuntu.com/ubuntu/ trusty/universe blast2 amd64 1:2.2.26.20120620-7 [640 kB] Get:27 http://archive.ubuntu.com/ubuntu/ trusty/universe bwa amd64 0.7.5a-2 [170 kB] Get:28 http://archive.ubuntu.com/ubuntu/ trusty/multiverse clustalw amd64 2.1+lgpl-4 [270 kB] Get:29 http://archive.ubuntu.com/ubuntu/ trusty/universe dialign amd64 2.2.1-6 [204 kB] Get:30 http://archive.ubuntu.com/ubuntu/ trusty/universe libhpdf-2.2.1 amd64 2.2.1-1ubuntu2 [334 kB] Get:31 http://archive.ubuntu.com/ubuntu/ trusty/universe emboss-lib amd64 6.6.0-1 [3082 kB] Get:32 http://archive.ubuntu.com/ubuntu/ trusty/universe emboss-data all 6.6.0-1 [60.8 MB] Get:33 http://archive.ubuntu.com/ubuntu/ trusty/universe emboss amd64 6.6.0-1 [953 kB] Get:34 http://archive.ubuntu.com/ubuntu/ trusty/universe exonerate amd64 2.2.0-6 [3107 kB] Get:35 http://archive.ubuntu.com/ubuntu/ trusty/main libijs-0.35 amd64 0.35-8build1 [16.8 kB] Get:36 http://archive.ubuntu.com/ubuntu/ trusty-updates/main libjbig2dec0 amd64 0.11+20120125-1ubuntu1.1 [43.0 kB] Get:37 http://archive.ubuntu.com/ubuntu/ trusty-updates/main libgs9-common all 9.26~dfsg+0-0ubuntu0.14.04.8 [5098 kB] Get:38 http://archive.ubuntu.com/ubuntu/ trusty-updates/main libgs9 amd64 9.26~dfsg+0-0ubuntu0.14.04.8 [2355 kB] Get:39 http://archive.ubuntu.com/ubuntu/ trusty/main gsfonts all 1:8.11+urwcyr1.0.7~pre44-4.2ubuntu1 [3374 kB] Get:40 http://archive.ubuntu.com/ubuntu/ trusty-updates/main ghostscript amd64 9.26~dfsg+0-0ubuntu0.14.04.8 [47.1 kB] Get:41 http://archive.ubuntu.com/ubuntu/ trusty/universe infernal amd64 1.1~rc4-2 [1800 kB] Get:42 http://archive.ubuntu.com/ubuntu/ trusty/universe kalign amd64 1:2.03+20110620-2 [102 kB] Get:43 http://archive.ubuntu.com/ubuntu/ trusty/main libipc-sharelite-perl amd64 0.17-3build1 [25.5 kB] Get:44 http://archive.ubuntu.com/ubuntu/ trusty/universe libcache-cache-perl all 1.06-2 [75.8 kB] Get:45 http://archive.ubuntu.com/ubuntu/ trusty/universe libace-perl amd64 1.92-3 [352 kB] Get:46 http://archive.ubuntu.com/ubuntu/ trusty/main libalgorithm-c3-perl all 0.08-1 [11.8 kB] Get:47 http://archive.ubuntu.com/ubuntu/ trusty/universe libalgorithm-munkres-perl all 0.08-2 [12.4 kB] Get:48 http://archive.ubuntu.com/ubuntu/ trusty-updates/main libperl5.18 amd64 5.18.2-2ubuntu1.7 [1330 B] Get:49 http://archive.ubuntu.com/ubuntu/ trusty/main libdevel-symdump-perl all 2.11-2 [13.4 kB] Get:50 http://archive.ubuntu.com/ubuntu/ trusty-updates/main libapache2-mod-perl2 amd64 2.0.8+httpd24-r1449661-6ubuntu2.1 [848 kB] Get:51 http://archive.ubuntu.com/ubuntu/ trusty/universe libapache-dbi-perl all 1.12-1 [47.0 kB] Get:52 http://archive.ubuntu.com/ubuntu/ trusty/main libapache2-reload-perl all 0.12-2 [17.3 kB] Get:53 http://archive.ubuntu.com/ubuntu/ trusty/main libparams-util-perl amd64 1.07-1build1 [22.4 kB] Get:54 http://archive.ubuntu.com/ubuntu/ trusty/main libsub-install-perl all 0.927-1 [10.6 kB] Get:55 http://archive.ubuntu.com/ubuntu/ trusty/main libdata-optlist-perl all 0.109-1 [9920 B] Get:56 http://archive.ubuntu.com/ubuntu/ trusty/main libparams-classify-perl amd64 0.013-4build2 [23.0 kB] Get:57 http://archive.ubuntu.com/ubuntu/ trusty/main libmodule-runtime-perl all 0.013-1 [15.8 kB] Get:58 http://archive.ubuntu.com/ubuntu/ trusty/main libtry-tiny-perl all 0.19-1 [17.6 kB] Get:59 http://archive.ubuntu.com/ubuntu/ trusty/main libmodule-implementation-perl all 0.07-1 [12.8 kB] Get:60 http://archive.ubuntu.com/ubuntu/ trusty/main libpackage-stash-perl all 0.36-1 [21.7 kB] Get:61 http://archive.ubuntu.com/ubuntu/ trusty/main libclass-load-perl all 0.20-1 [11.6 kB] Get:62 http://archive.ubuntu.com/ubuntu/ trusty/main libclass-load-xs-perl amd64 0.06-1build1 [13.9 kB] Get:63 http://archive.ubuntu.com/ubuntu/ trusty/main libsub-exporter-progressive-perl all 0.001011-1 [7064 B] Get:64 http://archive.ubuntu.com/ubuntu/ trusty/main libdevel-globaldestruction-perl all 0.12-1 [7858 B] Get:65 http://archive.ubuntu.com/ubuntu/ trusty/main libsub-exporter-perl all 0.986-1 [50.6 kB] Get:66 http://archive.ubuntu.com/ubuntu/ trusty/main libeval-closure-perl all 0.11-1 [11.3 kB] Get:67 http://archive.ubuntu.com/ubuntu/ trusty/main libclass-c3-perl all 0.25-1 [21.5 kB] Get:68 http://archive.ubuntu.com/ubuntu/ trusty/main libmro-compat-perl all 0.12-1 [12.2 kB] Get:69 http://archive.ubuntu.com/ubuntu/ trusty/main libpackage-deprecationmanager-perl all 0.13-1 [12.9 kB] Get:70 http://archive.ubuntu.com/ubuntu/ trusty/main libpackage-stash-xs-perl amd64 0.28-1 [18.7 kB] Get:71 http://archive.ubuntu.com/ubuntu/ trusty/main libsub-name-perl amd64 0.05-1build4 [9774 B] Get:72 http://archive.ubuntu.com/ubuntu/ trusty/main libtask-weaken-perl all 1.04-1 [7628 B] Get:73 http://archive.ubuntu.com/ubuntu/ trusty/main libmoose-perl amd64 2.1005-1 [849 kB] Get:74 http://archive.ubuntu.com/ubuntu/ trusty/universe libarray-compare-perl all 2.02-1 [13.4 kB] Get:75 http://archive.ubuntu.com/ubuntu/ trusty/main libvariable-magic-perl amd64 0.53-1 [36.2 kB] Get:76 http://archive.ubuntu.com/ubuntu/ trusty/main libb-hooks-endofscope-perl all 0.13-1 [14.4 kB] Get:77 http://archive.ubuntu.com/ubuntu/ trusty/universe libbio-asn1-entrezgene-perl all 1.700-1 [41.8 kB] Get:78 http://archive.ubuntu.com/ubuntu/ trusty/main libcarp-clan-perl all 6.04-1 [14.1 kB] Get:79 http://archive.ubuntu.com/ubuntu/ trusty/main libbit-vector-perl amd64 7.3-1build1 [160 kB] Get:80 http://archive.ubuntu.com/ubuntu/ trusty/main libclass-c3-xs-perl amd64 0.13-1build4 [15.1 kB] Get:81 http://archive.ubuntu.com/ubuntu/ trusty/main libclass-inspector-perl all 1.28-1 [18.7 kB] Get:82 http://archive.ubuntu.com/ubuntu/ trusty/main libclass-tiny-perl all 0.012-1 [14.9 kB] Get:83 http://archive.ubuntu.com/ubuntu/ trusty/main libclone-perl amd64 0.36-1 [11.0 kB] Get:84 http://archive.ubuntu.com/ubuntu/ trusty/universe libconvert-binary-c-perl amd64 0.76-3build1 [299 kB] Get:85 http://archive.ubuntu.com/ubuntu/ trusty/main libconvert-binhex-perl all 1.123-1 [32.2 kB] Get:86 http://archive.ubuntu.com/ubuntu/ trusty/universe libcrypt-ssleay-perl amd64 0.58-1build1 [40.4 kB] Get:87 http://archive.ubuntu.com/ubuntu/ trusty/universe libdate-calc-perl all 6.3-1 [209 kB] Get:88 http://archive.ubuntu.com/ubuntu/ trusty/universe libdate-calc-xs-perl amd64 6.3-1build1 [56.0 kB] Get:89 http://archive.ubuntu.com/ubuntu/ trusty/main libdate-manip-perl all 6.42-1 [913 kB] Get:90 http://archive.ubuntu.com/ubuntu/ trusty/main libpadwalker-perl amd64 1.98-1 [17.1 kB] Get:91 http://archive.ubuntu.com/ubuntu/ trusty/main libdevel-caller-perl amd64 2.06-1build1 [12.1 kB] Get:92 http://archive.ubuntu.com/ubuntu/ trusty/main libdevel-lexalias-perl amd64 0.05-1build1 [9962 B] Get:93 http://archive.ubuntu.com/ubuntu/ trusty/main libsub-identify-perl amd64 0.04-1build3 [9254 B] Get:94 http://archive.ubuntu.com/ubuntu/ trusty/main libnamespace-clean-perl all 0.24-1 [13.0 kB] Get:95 http://archive.ubuntu.com/ubuntu/ trusty/main libdevel-partialdump-perl all 0.17-1 [13.6 kB] Get:96 http://archive.ubuntu.com/ubuntu/ trusty/universe libfcgi-perl amd64 0.74-1build2 [36.8 kB] Get:97 http://archive.ubuntu.com/ubuntu/ trusty/universe libfreezethaw-perl all 0.5001-1 [18.2 kB] Get:98 http://archive.ubuntu.com/ubuntu/ trusty/universe libheap-perl all 0.80-2 [40.4 kB] Get:99 http://archive.ubuntu.com/ubuntu/ trusty/universe libgraph-perl all 1:0.96-1.1 [127 kB] Get:100 http://archive.ubuntu.com/ubuntu/ trusty/main libio-pty-perl amd64 1:1.08-1build4 [36.9 kB] Get:101 http://archive.ubuntu.com/ubuntu/ trusty/main libipc-run-perl all 0.92-1 [101 kB] Get:102 http://archive.ubuntu.com/ubuntu/ trusty/universe libxml-twig-perl all 1:3.44-1 [154 kB] Get:103 http://archive.ubuntu.com/ubuntu/ trusty/universe libxml-xpath-perl all 1.13-7 [80.7 kB] Get:104 http://archive.ubuntu.com/ubuntu/ trusty/main libparse-recdescent-perl all 1.967009+dfsg-1 [158 kB] Get:105 http://archive.ubuntu.com/ubuntu/ trusty/universe libgraphviz-perl all 2.14-1 [111 kB] Get:106 http://archive.ubuntu.com/ubuntu/ trusty/universe libhtml-tableextract-perl all 2.11-1 [29.8 kB] Get:107 http://archive.ubuntu.com/ubuntu/ trusty/universe libio-sessiondata-perl all 1.03-1 [5606 B] Get:108 http://archive.ubuntu.com/ubuntu/ trusty/main libio-stringy-perl all 2.110-5 [93.5 kB] Get:109 http://archive.ubuntu.com/ubuntu/ trusty/universe libjcode-pm-perl amd64 2.06-1 [31.0 kB] Get:110 http://archive.ubuntu.com/ubuntu/ trusty/universe libmath-derivative-perl all 0.01-6 [6260 B] Get:111 http://archive.ubuntu.com/ubuntu/ trusty/universe libmath-spline-perl all 0.02-1 [7966 B] Get:112 http://archive.ubuntu.com/ubuntu/ trusty/main libmime-tools-perl all 5.505-1 [206 kB] Get:113 http://archive.ubuntu.com/ubuntu/ trusty/universe libmldbm-perl all 2.05-1 [18.3 kB] Get:114 http://archive.ubuntu.com/ubuntu/ trusty/universe libole-storage-lite-perl all 0.19-1 [26.1 kB] Get:115 http://archive.ubuntu.com/ubuntu/ trusty/main libossp-uuid16 amd64 1.6.2-1.3ubuntu1 [29.6 kB] Get:116 http://archive.ubuntu.com/ubuntu/ trusty/universe libossp-uuid-perl amd64 1.6.2-1.3ubuntu1 [19.8 kB] Get:117 http://archive.ubuntu.com/ubuntu/ trusty/universe libpostscript-perl all 0.06-2 [31.2 kB] Get:118 http://archive.ubuntu.com/ubuntu/ trusty/main ruby all 1:1.9.3.4 [5334 B] Get:119 http://archive.ubuntu.com/ubuntu/ trusty-updates/main ruby1.9.1 amd64 1.9.3.484-2ubuntu1.14 [35.6 kB] Get:120 http://archive.ubuntu.com/ubuntu/ trusty-updates/main libruby1.9.1 amd64 1.9.3.484-2ubuntu1.14 [2648 kB] Get:121 http://archive.ubuntu.com/ubuntu/ trusty/universe libsoap-lite-perl all 1.09-1 [253 kB] Get:122 http://archive.ubuntu.com/ubuntu/ trusty/universe libsort-naturally-perl all 1.02-1 [14.4 kB] Get:123 http://archive.ubuntu.com/ubuntu/ trusty/universe libspreadsheet-writeexcel-perl all 2.40-1 [628 kB] Get:124 http://archive.ubuntu.com/ubuntu/ trusty/universe libunicode-map-perl amd64 0.112-11 [143 kB] Get:125 http://archive.ubuntu.com/ubuntu/ trusty/universe libspreadsheet-parseexcel-perl all 0.5800-1 [160 kB] Get:126 http://archive.ubuntu.com/ubuntu/ trusty/universe libstatistics-descriptive-perl all 3.0605-1 [38.7 kB] Get:127 http://archive.ubuntu.com/ubuntu/ trusty/universe libsvg-perl all 2.59-1 [79.0 kB] Get:128 http://archive.ubuntu.com/ubuntu/ trusty/main libfile-slurp-perl all 9999.19-4 [41.3 kB] Get:129 http://archive.ubuntu.com/ubuntu/ trusty/main libtree-dagnode-perl all 1.17-1 [59.6 kB] Get:130 http://archive.ubuntu.com/ubuntu/ trusty/universe libsvg-graph-perl all 0.02-2 [128 kB] Get:131 http://archive.ubuntu.com/ubuntu/ trusty/main libtie-ixhash-perl all 1.23-1 [11.7 kB] Get:132 http://archive.ubuntu.com/ubuntu/ trusty/main libxml-perl all 0.08-2 [113 kB] Get:133 http://archive.ubuntu.com/ubuntu/ trusty/main libxml-regexp-perl all 0.04-1 [8072 B] Get:134 http://archive.ubuntu.com/ubuntu/ trusty/main libxml-dom-perl all 1.44-1 [185 kB] Get:135 http://archive.ubuntu.com/ubuntu/ trusty/universe libxml-xpathengine-perl all 0.13-1 [37.1 kB] Get:136 http://archive.ubuntu.com/ubuntu/ trusty/universe libxml-dom-xpath-perl all 0.14-1 [9722 B] Get:137 http://archive.ubuntu.com/ubuntu/ trusty/main libxml-namespacesupport-perl all 1.11-1 [13.2 kB] Get:138 http://archive.ubuntu.com/ubuntu/ trusty/main libxml-sax-base-perl all 1.07-1 [21.5 kB] Get:139 http://archive.ubuntu.com/ubuntu/ trusty/main libxml-sax-perl all 0.99+dfsg-2ubuntu1 [64.6 kB] Get:140 http://archive.ubuntu.com/ubuntu/ trusty/main libxml-filter-buffertext-perl all 1.01-5 [7374 B] Get:141 http://archive.ubuntu.com/ubuntu/ trusty-updates/main libxml-libxml-perl amd64 2.0108+dfsg-1ubuntu0.2 [336 kB] Get:142 http://archive.ubuntu.com/ubuntu/ trusty/main libxml-libxslt-perl amd64 1.84-1 [42.3 kB] Get:143 http://archive.ubuntu.com/ubuntu/ trusty/main libxml-sax-expat-perl all 0.40-2 [11.5 kB] Get:144 http://archive.ubuntu.com/ubuntu/ trusty/main libxml-sax-writer-perl all 0.53-1 [22.3 kB] Get:145 http://archive.ubuntu.com/ubuntu/ trusty/main libxml-simple-perl all 2.20-1 [68.3 kB] Get:146 http://archive.ubuntu.com/ubuntu/ trusty/universe libxml-writer-perl all 0.623-1 [27.2 kB] Get:147 http://archive.ubuntu.com/ubuntu/ trusty/universe libxmlrpc-lite-perl all 0.717-1 [26.0 kB] Get:148 http://archive.ubuntu.com/ubuntu/ trusty-updates/main libyaml-libyaml-perl amd64 0.41-5ubuntu0.14.04.1 [63.8 kB] Get:149 http://archive.ubuntu.com/ubuntu/ trusty/main libyaml-perl all 0.84-1 [68.3 kB] Get:150 http://archive.ubuntu.com/ubuntu/ trusty/universe mafft amd64 7.123-1 [776 kB] Get:151 http://archive.ubuntu.com/ubuntu/ trusty/universe maq amd64 0.7.1-5 [298 kB] Get:152 http://archive.ubuntu.com/ubuntu/ trusty/universe muscle amd64 1:3.8.31-1 [169 kB] Get:153 http://archive.ubuntu.com/ubuntu/ trusty-updates/main perl-doc all 5.18.2-2ubuntu1.7 [7264 kB] Get:154 http://archive.ubuntu.com/ubuntu/ trusty/universe perl-tk amd64 1:804.031-1build1 [2619 kB] Get:155 http://archive.ubuntu.com/ubuntu/ trusty/universe phyml amd64 2:20120412-2 [1562 kB] Get:156 http://archive.ubuntu.com/ubuntu/ trusty/universe primer3 amd64 2.3.6-1 [169 kB] Get:157 http://archive.ubuntu.com/ubuntu/ trusty/universe probalign amd64 1.4-3 [81.4 kB] Get:158 http://archive.ubuntu.com/ubuntu/ trusty/universe probcons amd64 1.12-9 [228 kB] Get:159 http://archive.ubuntu.com/ubuntu/ trusty/universe samtools amd64 0.1.19-1 [560 kB] Get:160 http://archive.ubuntu.com/ubuntu/ trusty/universe sim4 amd64 0.0.20121010-1 [55.8 kB] Get:161 http://archive.ubuntu.com/ubuntu/ trusty/universe t-coffee amd64 10.00.r1613-1 [873 kB] Get:162 http://archive.ubuntu.com/ubuntu/ trusty/universe tigr-glimmer amd64 3.02-3 [446 kB] Get:163 http://archive.ubuntu.com/ubuntu/ trusty/universe tm-align amd64 20130511+dfsg-1 [66.4 kB] Get:164 http://archive.ubuntu.com/ubuntu/ trusty/universe bowtie amd64 1.0.0-5 [1276 kB] Get:165 http://archive.ubuntu.com/ubuntu/ trusty/universe hmmer amd64 3.1b1-3 [1022 kB] Get:166 http://archive.ubuntu.com/ubuntu/ trusty/main libbsd-resource-perl amd64 1.2907-1build1 [31.8 kB] Get:167 http://archive.ubuntu.com/ubuntu/ trusty/main libgd-gd2-perl amd64 1:2.46-3.1build1 [181 kB] Get:168 http://archive.ubuntu.com/ubuntu/ trusty/universe libset-scalar-perl all 1.27-1 [33.4 kB] Get:169 http://archive.ubuntu.com/ubuntu/ trusty/main lynx-cur amd64 2.8.8pre4-1 [956 kB] Get:170 http://archive.ubuntu.com/ubuntu/ trusty/main lynx all 2.8.8pre4-1 [4184 B] debconf: unable to initialize frontend: Dialog debconf: (TERM is not set, so the dialog frontend is not usable.) debconf: falling back to frontend: Readline debconf: unable to initialize frontend: Readline debconf: (This frontend requires a controlling tty.) debconf: falling back to frontend: Teletype dpkg-preconfigure: unable to re-open stdin: Fetched 134 MB in 40min 11s (55.5 kB/s) Selecting previously unselected package libapr1:amd64. (Reading database ... 30278 files and directories currently installed.) Preparing to unpack .../libapr1_1.5.0-1_amd64.deb ... Unpacking libapr1:amd64 (1.5.0-1) ... Selecting previously unselected package libaprutil1:amd64. Preparing to unpack .../libaprutil1_1.5.3-1_amd64.deb ... Unpacking libaprutil1:amd64 (1.5.3-1) ... Selecting previously unselected package libavahi-common-data:amd64. Preparing to unpack .../libavahi-common-data_0.6.31-4ubuntu1.3_amd64.deb ... Unpacking libavahi-common-data:amd64 (0.6.31-4ubuntu1.3) ... Selecting previously unselected package libavahi-common3:amd64. Preparing to unpack .../libavahi-common3_0.6.31-4ubuntu1.3_amd64.deb ... Unpacking libavahi-common3:amd64 (0.6.31-4ubuntu1.3) ... Selecting previously unselected package libavahi-client3:amd64. Preparing to unpack .../libavahi-client3_0.6.31-4ubuntu1.3_amd64.deb ... Unpacking libavahi-client3:amd64 (0.6.31-4ubuntu1.3) ... Selecting previously unselected package libcups2:amd64. Preparing to unpack .../libcups2_1.7.2-0ubuntu1.11_amd64.deb ... Unpacking libcups2:amd64 (1.7.2-0ubuntu1.11) ... Selecting previously unselected package libcupsfilters1:amd64. Preparing to unpack .../libcupsfilters1_1.0.52-0ubuntu1.8_amd64.deb ... Unpacking libcupsfilters1:amd64 (1.0.52-0ubuntu1.8) ... Selecting previously unselected package libcupsimage2:amd64. Preparing to unpack .../libcupsimage2_1.7.2-0ubuntu1.11_amd64.deb ... Unpacking libcupsimage2:amd64 (1.7.2-0ubuntu1.11) ... Selecting previously unselected package ncbi-data. Preparing to unpack .../ncbi-data_6.1.20120620-7_all.deb ... Unpacking ncbi-data (6.1.20120620-7) ... Selecting previously unselected package libncbi6:amd64. Preparing to unpack .../libncbi6_6.1.20120620-7_amd64.deb ... Unpacking libncbi6:amd64 (6.1.20120620-7) ... Selecting previously unselected package libyaml-0-2:amd64. Preparing to unpack .../libyaml-0-2_0.1.4-3ubuntu3.1_amd64.deb ... Unpacking libyaml-0-2:amd64 (0.1.4-3ubuntu3.1) ... Selecting previously unselected package poppler-data. Preparing to unpack .../poppler-data_0.4.6-4_all.deb ... Unpacking poppler-data (0.4.6-4) ... Selecting previously unselected package wise-data. Preparing to unpack .../wise-data_2.4.1-14_all.deb ... Unpacking wise-data (2.4.1-14) ... Selecting previously unselected package wise. Preparing to unpack .../wise_2.4.1-14_amd64.deb ... Unpacking wise (2.4.1-14) ... Selecting previously unselected package amap-align. Preparing to unpack .../amap-align_2.2-4_amd64.deb ... Unpacking amap-align (2.2-4) ... Selecting previously unselected package libaprutil1-dbd-sqlite3:amd64. Preparing to unpack .../libaprutil1-dbd-sqlite3_1.5.3-1_amd64.deb ... Unpacking libaprutil1-dbd-sqlite3:amd64 (1.5.3-1) ... Selecting previously unselected package libaprutil1-ldap:amd64. Preparing to unpack .../libaprutil1-ldap_1.5.3-1_amd64.deb ... Unpacking libaprutil1-ldap:amd64 (1.5.3-1) ... Selecting previously unselected package apache2-bin. Preparing to unpack .../apache2-bin_2.4.7-1ubuntu4.22_amd64.deb ... Unpacking apache2-bin (2.4.7-1ubuntu4.22) ... Selecting previously unselected package bedtools. Preparing to unpack .../bedtools_2.17.0-1_amd64.deb ... Unpacking bedtools (2.17.0-1) ... Selecting previously unselected package libio-string-perl. Preparing to unpack .../libio-string-perl_1.08-3_all.deb ... Unpacking libio-string-perl (1.08-3) ... Selecting previously unselected package libdata-stag-perl. Preparing to unpack .../libdata-stag-perl_0.13-1_all.deb ... Unpacking libdata-stag-perl (0.13-1) ... Selecting previously unselected package libbio-perl-perl. Preparing to unpack .../libbio-perl-perl_1.6.923-1_all.deb ... Unpacking libbio-perl-perl (1.6.923-1) ... Selecting previously unselected package bioperl. Preparing to unpack .../bioperl_1.6.923-1_all.deb ... Unpacking bioperl (1.6.923-1) ... Selecting previously unselected package libbio-perl-run-perl. Preparing to unpack .../libbio-perl-run-perl_1.6.9-2_all.deb ... Unpacking libbio-perl-run-perl (1.6.9-2) ... Selecting previously unselected package bioperl-run. Preparing to unpack .../bioperl-run_1.6.9-2_all.deb ... Unpacking bioperl-run (1.6.9-2) ... Selecting previously unselected package blast2. Preparing to unpack .../blast2_1%3a2.2.26.20120620-7_amd64.deb ... Unpacking blast2 (1:2.2.26.20120620-7) ... Selecting previously unselected package bwa. Preparing to unpack .../bwa_0.7.5a-2_amd64.deb ... Unpacking bwa (0.7.5a-2) ... Selecting previously unselected package clustalw. Preparing to unpack .../clustalw_2.1+lgpl-4_amd64.deb ... Unpacking clustalw (2.1+lgpl-4) ... Selecting previously unselected package dialign. Preparing to unpack .../dialign_2.2.1-6_amd64.deb ... Unpacking dialign (2.2.1-6) ... Selecting previously unselected package libhpdf-2.2.1. Preparing to unpack .../libhpdf-2.2.1_2.2.1-1ubuntu2_amd64.deb ... Unpacking libhpdf-2.2.1 (2.2.1-1ubuntu2) ... Selecting previously unselected package emboss-lib. Preparing to unpack .../emboss-lib_6.6.0-1_amd64.deb ... Unpacking emboss-lib (6.6.0-1) ... Selecting previously unselected package emboss-data. Preparing to unpack .../emboss-data_6.6.0-1_all.deb ... Unpacking emboss-data (6.6.0-1) ... Selecting previously unselected package emboss. Preparing to unpack .../emboss_6.6.0-1_amd64.deb ... Unpacking emboss (6.6.0-1) ... Selecting previously unselected package exonerate. Preparing to unpack .../exonerate_2.2.0-6_amd64.deb ... Unpacking exonerate (2.2.0-6) ... Selecting previously unselected package libijs-0.35. Preparing to unpack .../libijs-0.35_0.35-8build1_amd64.deb ... Unpacking libijs-0.35 (0.35-8build1) ... Selecting previously unselected package libjbig2dec0. Preparing to unpack .../libjbig2dec0_0.11+20120125-1ubuntu1.1_amd64.deb ... Unpacking libjbig2dec0 (0.11+20120125-1ubuntu1.1) ... Selecting previously unselected package libgs9-common. Preparing to unpack .../libgs9-common_9.26~dfsg+0-0ubuntu0.14.04.8_all.deb ... Unpacking libgs9-common (9.26~dfsg+0-0ubuntu0.14.04.8) ... Selecting previously unselected package libgs9. Preparing to unpack .../libgs9_9.26~dfsg+0-0ubuntu0.14.04.8_amd64.deb ... Unpacking libgs9 (9.26~dfsg+0-0ubuntu0.14.04.8) ... Selecting previously unselected package gsfonts. Preparing to unpack .../gsfonts_1%3a8.11+urwcyr1.0.7~pre44-4.2ubuntu1_all.deb ... Unpacking gsfonts (1:8.11+urwcyr1.0.7~pre44-4.2ubuntu1) ... Selecting previously unselected package ghostscript. Preparing to unpack .../ghostscript_9.26~dfsg+0-0ubuntu0.14.04.8_amd64.deb ... Unpacking ghostscript (9.26~dfsg+0-0ubuntu0.14.04.8) ... Selecting previously unselected package infernal. Preparing to unpack .../infernal_1.1~rc4-2_amd64.deb ... Unpacking infernal (1.1~rc4-2) ... Selecting previously unselected package kalign. Preparing to unpack .../kalign_1%3a2.03+20110620-2_amd64.deb ... Unpacking kalign (1:2.03+20110620-2) ... Selecting previously unselected package libipc-sharelite-perl. Preparing to unpack .../libipc-sharelite-perl_0.17-3build1_amd64.deb ... Unpacking libipc-sharelite-perl (0.17-3build1) ... Selecting previously unselected package libcache-cache-perl. Preparing to unpack .../libcache-cache-perl_1.06-2_all.deb ... Unpacking libcache-cache-perl (1.06-2) ... Selecting previously unselected package libace-perl. Preparing to unpack .../libace-perl_1.92-3_amd64.deb ... Unpacking libace-perl (1.92-3) ... Selecting previously unselected package libalgorithm-c3-perl. Preparing to unpack .../libalgorithm-c3-perl_0.08-1_all.deb ... Unpacking libalgorithm-c3-perl (0.08-1) ... Selecting previously unselected package libalgorithm-munkres-perl. Preparing to unpack .../libalgorithm-munkres-perl_0.08-2_all.deb ... Unpacking libalgorithm-munkres-perl (0.08-2) ... Selecting previously unselected package libperl5.18. Preparing to unpack .../libperl5.18_5.18.2-2ubuntu1.7_amd64.deb ... Unpacking libperl5.18 (5.18.2-2ubuntu1.7) ... Selecting previously unselected package libdevel-symdump-perl. Preparing to unpack .../libdevel-symdump-perl_2.11-2_all.deb ... Unpacking libdevel-symdump-perl (2.11-2) ... Selecting previously unselected package libapache2-mod-perl2. Preparing to unpack .../libapache2-mod-perl2_2.0.8+httpd24-r1449661-6ubuntu2.1_amd64.deb ... Unpacking libapache2-mod-perl2 (2.0.8+httpd24-r1449661-6ubuntu2.1) ... Selecting previously unselected package libapache-dbi-perl. Preparing to unpack .../libapache-dbi-perl_1.12-1_all.deb ... Unpacking libapache-dbi-perl (1.12-1) ... Selecting previously unselected package libapache2-reload-perl. Preparing to unpack .../libapache2-reload-perl_0.12-2_all.deb ... Unpacking libapache2-reload-perl (0.12-2) ... Selecting previously unselected package libparams-util-perl. Preparing to unpack .../libparams-util-perl_1.07-1build1_amd64.deb ... Unpacking libparams-util-perl (1.07-1build1) ... Selecting previously unselected package libsub-install-perl. Preparing to unpack .../libsub-install-perl_0.927-1_all.deb ... Unpacking libsub-install-perl (0.927-1) ... Selecting previously unselected package libdata-optlist-perl. Preparing to unpack .../libdata-optlist-perl_0.109-1_all.deb ... Unpacking libdata-optlist-perl (0.109-1) ... Selecting previously unselected package libparams-classify-perl. Preparing to unpack .../libparams-classify-perl_0.013-4build2_amd64.deb ... Unpacking libparams-classify-perl (0.013-4build2) ... Selecting previously unselected package libmodule-runtime-perl. Preparing to unpack .../libmodule-runtime-perl_0.013-1_all.deb ... Unpacking libmodule-runtime-perl (0.013-1) ... Selecting previously unselected package libtry-tiny-perl. Preparing to unpack .../libtry-tiny-perl_0.19-1_all.deb ... Unpacking libtry-tiny-perl (0.19-1) ... Selecting previously unselected package libmodule-implementation-perl. Preparing to unpack .../libmodule-implementation-perl_0.07-1_all.deb ... Unpacking libmodule-implementation-perl (0.07-1) ... Selecting previously unselected package libpackage-stash-perl. Preparing to unpack .../libpackage-stash-perl_0.36-1_all.deb ... Unpacking libpackage-stash-perl (0.36-1) ... Selecting previously unselected package libclass-load-perl. Preparing to unpack .../libclass-load-perl_0.20-1_all.deb ... Unpacking libclass-load-perl (0.20-1) ... Selecting previously unselected package libclass-load-xs-perl. Preparing to unpack .../libclass-load-xs-perl_0.06-1build1_amd64.deb ... Unpacking libclass-load-xs-perl (0.06-1build1) ... Selecting previously unselected package libsub-exporter-progressive-perl. Preparing to unpack .../libsub-exporter-progressive-perl_0.001011-1_all.deb ... Unpacking libsub-exporter-progressive-perl (0.001011-1) ... Selecting previously unselected package libdevel-globaldestruction-perl. Preparing to unpack .../libdevel-globaldestruction-perl_0.12-1_all.deb ... Unpacking libdevel-globaldestruction-perl (0.12-1) ... Selecting previously unselected package libsub-exporter-perl. Preparing to unpack .../libsub-exporter-perl_0.986-1_all.deb ... Unpacking libsub-exporter-perl (0.986-1) ... Selecting previously unselected package libeval-closure-perl. Preparing to unpack .../libeval-closure-perl_0.11-1_all.deb ... Unpacking libeval-closure-perl (0.11-1) ... Selecting previously unselected package libclass-c3-perl. Preparing to unpack .../libclass-c3-perl_0.25-1_all.deb ... Unpacking libclass-c3-perl (0.25-1) ... Selecting previously unselected package libmro-compat-perl. Preparing to unpack .../libmro-compat-perl_0.12-1_all.deb ... Unpacking libmro-compat-perl (0.12-1) ... Selecting previously unselected package libpackage-deprecationmanager-perl. Preparing to unpack .../libpackage-deprecationmanager-perl_0.13-1_all.deb ... Unpacking libpackage-deprecationmanager-perl (0.13-1) ... Selecting previously unselected package libpackage-stash-xs-perl. Preparing to unpack .../libpackage-stash-xs-perl_0.28-1_amd64.deb ... Unpacking libpackage-stash-xs-perl (0.28-1) ... Selecting previously unselected package libsub-name-perl. Preparing to unpack .../libsub-name-perl_0.05-1build4_amd64.deb ... Unpacking libsub-name-perl (0.05-1build4) ... Selecting previously unselected package libtask-weaken-perl. Preparing to unpack .../libtask-weaken-perl_1.04-1_all.deb ... Unpacking libtask-weaken-perl (1.04-1) ... Selecting previously unselected package libmoose-perl. Preparing to unpack .../libmoose-perl_2.1005-1_amd64.deb ... Unpacking libmoose-perl (2.1005-1) ... Selecting previously unselected package libarray-compare-perl. Preparing to unpack .../libarray-compare-perl_2.02-1_all.deb ... Unpacking libarray-compare-perl (2.02-1) ... Selecting previously unselected package libvariable-magic-perl. Preparing to unpack .../libvariable-magic-perl_0.53-1_amd64.deb ... Unpacking libvariable-magic-perl (0.53-1) ... Selecting previously unselected package libb-hooks-endofscope-perl. Preparing to unpack .../libb-hooks-endofscope-perl_0.13-1_all.deb ... Unpacking libb-hooks-endofscope-perl (0.13-1) ... Selecting previously unselected package libbio-asn1-entrezgene-perl. Preparing to unpack .../libbio-asn1-entrezgene-perl_1.700-1_all.deb ... Unpacking libbio-asn1-entrezgene-perl (1.700-1) ... Selecting previously unselected package libcarp-clan-perl. Preparing to unpack .../libcarp-clan-perl_6.04-1_all.deb ... Unpacking libcarp-clan-perl (6.04-1) ... Selecting previously unselected package libbit-vector-perl. Preparing to unpack .../libbit-vector-perl_7.3-1build1_amd64.deb ... Unpacking libbit-vector-perl (7.3-1build1) ... Selecting previously unselected package libclass-c3-xs-perl. Preparing to unpack .../libclass-c3-xs-perl_0.13-1build4_amd64.deb ... Unpacking libclass-c3-xs-perl (0.13-1build4) ... Selecting previously unselected package libclass-inspector-perl. Preparing to unpack .../libclass-inspector-perl_1.28-1_all.deb ... Unpacking libclass-inspector-perl (1.28-1) ... Selecting previously unselected package libclass-tiny-perl. Preparing to unpack .../libclass-tiny-perl_0.012-1_all.deb ... Unpacking libclass-tiny-perl (0.012-1) ... Selecting previously unselected package libclone-perl. Preparing to unpack .../libclone-perl_0.36-1_amd64.deb ... Unpacking libclone-perl (0.36-1) ... Selecting previously unselected package libconvert-binary-c-perl. Preparing to unpack .../libconvert-binary-c-perl_0.76-3build1_amd64.deb ... Unpacking libconvert-binary-c-perl (0.76-3build1) ... Selecting previously unselected package libconvert-binhex-perl. Preparing to unpack .../libconvert-binhex-perl_1.123-1_all.deb ... Unpacking libconvert-binhex-perl (1.123-1) ... Selecting previously unselected package libcrypt-ssleay-perl. 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Setting up libcupsimage2:amd64 (1.7.2-0ubuntu1.11) ... Setting up ncbi-data (6.1.20120620-7) ... Setting up libncbi6:amd64 (6.1.20120620-7) ... Setting up libyaml-0-2:amd64 (0.1.4-3ubuntu3.1) ... Setting up poppler-data (0.4.6-4) ... Setting up wise-data (2.4.1-14) ... Setting up wise (2.4.1-14) ... Setting up amap-align (2.2-4) ... Setting up libaprutil1-dbd-sqlite3:amd64 (1.5.3-1) ... Setting up libaprutil1-ldap:amd64 (1.5.3-1) ... Setting up apache2-bin (2.4.7-1ubuntu4.22) ... Setting up bedtools (2.17.0-1) ... Setting up libio-string-perl (1.08-3) ... Setting up libdata-stag-perl (0.13-1) ... Setting up libbio-perl-perl (1.6.923-1) ... Setting up bioperl (1.6.923-1) ... Setting up libbio-perl-run-perl (1.6.9-2) ... Setting up bioperl-run (1.6.9-2) ... Setting up blast2 (1:2.2.26.20120620-7) ... Setting up bwa (0.7.5a-2) ... Setting up clustalw (2.1+lgpl-4) ... Setting up dialign (2.2.1-6) ... Setting up libhpdf-2.2.1 (2.2.1-1ubuntu2) ... Setting up emboss-lib (6.6.0-1) ... Setting up emboss-data (6.6.0-1) ... Setting up emboss (6.6.0-1) ... Setting up exonerate (2.2.0-6) ... Setting up libijs-0.35 (0.35-8build1) ... Setting up libjbig2dec0 (0.11+20120125-1ubuntu1.1) ... Setting up libgs9-common (9.26~dfsg+0-0ubuntu0.14.04.8) ... update-alternatives: using /usr/share/ghostscript/9.26 to provide /usr/share/ghostscript/current (ghostscript-current) in auto mode Setting up libgs9 (9.26~dfsg+0-0ubuntu0.14.04.8) ... Setting up gsfonts (1:8.11+urwcyr1.0.7~pre44-4.2ubuntu1) ... Setting up ghostscript (9.26~dfsg+0-0ubuntu0.14.04.8) ... Setting up infernal (1.1~rc4-2) ... Setting up kalign (1:2.03+20110620-2) ... Setting up libipc-sharelite-perl (0.17-3build1) ... Setting up libcache-cache-perl (1.06-2) ... Setting up libace-perl (1.92-3) ... Setting up libalgorithm-c3-perl (0.08-1) ... Setting up libalgorithm-munkres-perl (0.08-2) ... Setting up libperl5.18 (5.18.2-2ubuntu1.7) ... Setting up libdevel-symdump-perl (2.11-2) ... Setting up libapache2-mod-perl2 (2.0.8+httpd24-r1449661-6ubuntu2.1) ... Setting up libapache-dbi-perl (1.12-1) ... Setting up libapache2-reload-perl (0.12-2) ... Setting up libparams-util-perl (1.07-1build1) ... Setting up libsub-install-perl (0.927-1) ... Setting up libdata-optlist-perl (0.109-1) ... Setting up libparams-classify-perl (0.013-4build2) ... Setting up libmodule-runtime-perl (0.013-1) ... Setting up libtry-tiny-perl (0.19-1) ... Setting up libmodule-implementation-perl (0.07-1) ... Setting up libpackage-stash-perl (0.36-1) ... Setting up libclass-load-perl (0.20-1) ... Setting up libclass-load-xs-perl (0.06-1build1) ... Setting up libsub-exporter-progressive-perl (0.001011-1) ... Setting up libdevel-globaldestruction-perl (0.12-1) ... Setting up libsub-exporter-perl (0.986-1) ... Setting up libeval-closure-perl (0.11-1) ... Setting up libclass-c3-perl (0.25-1) ... Setting up libmro-compat-perl (0.12-1) ... Setting up libpackage-deprecationmanager-perl (0.13-1) ... Setting up libpackage-stash-xs-perl (0.28-1) ... Setting up libsub-name-perl (0.05-1build4) ... Setting up libtask-weaken-perl (1.04-1) ... Setting up libmoose-perl (2.1005-1) ... Setting up libarray-compare-perl (2.02-1) ... Setting up libvariable-magic-perl (0.53-1) ... Setting up libb-hooks-endofscope-perl (0.13-1) ... Setting up libbio-asn1-entrezgene-perl (1.700-1) ... Setting up libcarp-clan-perl (6.04-1) ... Setting up libbit-vector-perl (7.3-1build1) ... Setting up libclass-c3-xs-perl (0.13-1build4) ... Setting up libclass-inspector-perl (1.28-1) ... Setting up libclass-tiny-perl (0.012-1) ... Setting up libclone-perl (0.36-1) ... Setting up libconvert-binary-c-perl (0.76-3build1) ... Setting up libconvert-binhex-perl (1.123-1) ... Setting up libcrypt-ssleay-perl (0.58-1build1) ... Setting up libdate-calc-perl (6.3-1) ... Setting up libdate-calc-xs-perl (6.3-1build1) ... Setting up libdate-manip-perl (6.42-1) ... Setting up libpadwalker-perl (1.98-1) ... Setting up libdevel-caller-perl (2.06-1build1) ... Setting up libdevel-lexalias-perl (0.05-1build1) ... Setting up libsub-identify-perl (0.04-1build3) ... Setting up libnamespace-clean-perl (0.24-1) ... Setting up libdevel-partialdump-perl (0.17-1) ... Setting up libfcgi-perl (0.74-1build2) ... Setting up libfreezethaw-perl (0.5001-1) ... Setting up libheap-perl (0.80-2) ... Setting up libgraph-perl (1:0.96-1.1) ... Setting up libio-pty-perl (1:1.08-1build4) ... Setting up libipc-run-perl (0.92-1) ... Setting up libxml-twig-perl (1:3.44-1) ... Setting up libxml-xpath-perl (1.13-7) ... Setting up libparse-recdescent-perl (1.967009+dfsg-1) ... Setting up libgraphviz-perl (2.14-1) ... Setting up libhtml-tableextract-perl (2.11-1) ... Setting up libio-sessiondata-perl (1.03-1) ... Setting up libio-stringy-perl (2.110-5) ... Setting up libjcode-pm-perl (2.06-1) ... Setting up libmath-derivative-perl (0.01-6) ... Setting up libmath-spline-perl (0.02-1) ... Setting up libmime-tools-perl (5.505-1) ... Setting up libmldbm-perl (2.05-1) ... Setting up libole-storage-lite-perl (0.19-1) ... Setting up libossp-uuid16 (1.6.2-1.3ubuntu1) ... Setting up libossp-uuid-perl (1.6.2-1.3ubuntu1) ... Setting up libpostscript-perl (0.06-2) ... Setting up libsoap-lite-perl (1.09-1) ... Setting up libsort-naturally-perl (1.02-1) ... Setting up libspreadsheet-writeexcel-perl (2.40-1) ... Setting up libunicode-map-perl (0.112-11) ... Setting up libspreadsheet-parseexcel-perl (0.5800-1) ... Setting up libstatistics-descriptive-perl (3.0605-1) ... Setting up libsvg-perl (2.59-1) ... Setting up libfile-slurp-perl (9999.19-4) ... Setting up libtree-dagnode-perl (1.17-1) ... Setting up libsvg-graph-perl (0.02-2) ... Setting up libtie-ixhash-perl (1.23-1) ... Setting up libxml-perl (0.08-2) ... Setting up libxml-regexp-perl (0.04-1) ... Setting up libxml-dom-perl (1.44-1) ... Setting up libxml-xpathengine-perl (0.13-1) ... Setting up libxml-dom-xpath-perl (0.14-1) ... Setting up libxml-namespacesupport-perl (1.11-1) ... Setting up libxml-sax-base-perl (1.07-1) ... Setting up libxml-sax-perl (0.99+dfsg-2ubuntu1) ... update-perl-sax-parsers: Non-vendor version of XML::SAX is installed. update-perl-sax-parsers: Automatic registration of SAX parsers might not work. update-perl-sax-parsers: Registering Perl SAX parser XML::SAX::PurePerl with priority 10... update-perl-sax-parsers: Non-vendor version of XML::SAX is installed. update-perl-sax-parsers: Automatic registration of SAX parsers might not work. update-perl-sax-parsers: Updating overall Perl SAX parser modules info file... debconf: unable to initialize frontend: Dialog debconf: (TERM is not set, so the dialog frontend is not usable.) debconf: falling back to frontend: Readline debconf: unable to initialize frontend: Readline debconf: (This frontend requires a controlling tty.) debconf: falling back to frontend: Teletype Creating config file /etc/perl/XML/SAX/ParserDetails.ini with new version Setting up libxml-filter-buffertext-perl (1.01-5) ... Setting up libxml-libxml-perl (2.0108+dfsg-1ubuntu0.2) ... update-perl-sax-parsers: Non-vendor version of XML::SAX is installed. update-perl-sax-parsers: Automatic registration of SAX parsers might not work. update-perl-sax-parsers: Registering Perl SAX parser XML::LibXML::SAX::Parser with priority 50... update-perl-sax-parsers: Non-vendor version of XML::SAX is installed. update-perl-sax-parsers: Automatic registration of SAX parsers might not work. update-perl-sax-parsers: Registering Perl SAX parser XML::LibXML::SAX with priority 50... update-perl-sax-parsers: Non-vendor version of XML::SAX is installed. update-perl-sax-parsers: Automatic registration of SAX parsers might not work. update-perl-sax-parsers: Updating overall Perl SAX parser modules info file... debconf: unable to initialize frontend: Dialog debconf: (TERM is not set, so the dialog frontend is not usable.) debconf: falling back to frontend: Readline debconf: unable to initialize frontend: Readline debconf: (This frontend requires a controlling tty.) debconf: falling back to frontend: Teletype Replacing config file /etc/perl/XML/SAX/ParserDetails.ini with new version Setting up libxml-libxslt-perl (1.84-1) ... Setting up libxml-sax-expat-perl (0.40-2) ... update-perl-sax-parsers: Non-vendor version of XML::SAX is installed. update-perl-sax-parsers: Automatic registration of SAX parsers might not work. update-perl-sax-parsers: Registering Perl SAX parser XML::SAX::Expat with priority 50... update-perl-sax-parsers: Non-vendor version of XML::SAX is installed. update-perl-sax-parsers: Automatic registration of SAX parsers might not work. update-perl-sax-parsers: Updating overall Perl SAX parser modules info file... debconf: unable to initialize frontend: Dialog debconf: (TERM is not set, so the dialog frontend is not usable.) debconf: falling back to frontend: Readline debconf: unable to initialize frontend: Readline debconf: (This frontend requires a controlling tty.) debconf: falling back to frontend: Teletype Replacing config file /etc/perl/XML/SAX/ParserDetails.ini with new version Setting up libxml-sax-writer-perl (0.53-1) ... Setting up libxml-simple-perl (2.20-1) ... Setting up libxml-writer-perl (0.623-1) ... Setting up libxmlrpc-lite-perl (0.717-1) ... Setting up libyaml-libyaml-perl (0.41-5ubuntu0.14.04.1) ... Setting up libyaml-perl (0.84-1) ... Setting up mafft (7.123-1) ...]]> Jit https://bioinformaticsonline.com/snippets/view/41672/installing-busco-version-406 Wed, 13 May 2020 11:26:26 -0500 https://bioinformaticsonline.com/snippets/view/41672/installing-busco-version-406 (base) jit@jit-HP-Pro-3335-MT: conda install -c bioconda -c conda-forge busco=4.0.6 Collecting package metadata (repodata.json): done Solving environment: done ## Package Plan ## environment location: /home/jit/anaconda3 added / updated specs: - busco=4.0.6 The following packages will be downloaded: package | build ---------------------------|----------------- _r-mutex-1.0.1 | anacondar_1 3 KB conda-forge augustus-3.2.3 | pl526hcfae127_5 25.8 MB bioconda bamtools-2.4.1 | 1 737 KB bioconda binutils_impl_linux-64-2.34| h53a641e_0 9.2 MB conda-forge binutils_linux-64-2.34 | hc952b39_18 21 KB conda-forge biopython-1.76 | py37h516909a_0 2.6 MB conda-forge blast-2.2.31 | 1 131.2 MB bioconda busco-4.0.6 | pyr36_0 57 KB bioconda bwidget-1.9.14 | 0 119 KB conda-forge dendropy-4.4.0 | py_1 299 KB bioconda findutils-4.6.0 | h14c3975_1000 611 KB conda-forge gcc_impl_linux-64-7.3.0 | habb00fd_1 73.2 MB gcc_linux-64-7.3.0 | h553295d_18 22 KB conda-forge gettext-0.19.8.1 | hc5be6a0_1002 3.6 MB conda-forge gfortran_impl_linux-64-7.3.0| hdf63c60_5 9.4 MB conda-forge gfortran_linux-64-7.3.0 | h553295d_18 21 KB conda-forge gsl-2.2.1 | h0c605f7_3 2.6 MB gxx_impl_linux-64-7.3.0 | hdf63c60_1 18.7 MB gxx_linux-64-7.3.0 | h553295d_18 21 KB conda-forge hmmer-3.1b2 | 3 5.5 MB bioconda ld_impl_linux-64-2.34 | h53a641e_0 616 KB conda-forge libgfortran-3.0.0 | 1 281 KB conda-forge libpng-1.6.37 | hed695b0_1 308 KB conda-forge libssh2-1.9.0 | hab1572f_1 320 KB conda-forge lp_solve-5.5.2.5 | h14c3975_1001 419 KB conda-forge make-4.3 | h516909a_0 505 KB conda-forge metis-5.1.0 | he1b5a44_1005 4.1 MB conda-forge openblas-0.2.20 | 8 17.0 MB conda-forge perl-cpan-meta-2.150010 | pl526_0 5 KB bioconda perl-cpan-meta-requirements-2.140| pl526_0 12 KB bioconda perl-cpan-meta-yaml-0.018 | pl526_0 11 KB bioconda perl-extutils-cbuilder-0.280230| pl526_1 21 KB bioconda perl-extutils-manifest-1.72| pl526_0 13 KB bioconda perl-extutils-parsexs-3.35 | pl526_0 38 KB bioconda perl-json-pp-4.04 | pl526_0 30 KB bioconda perl-module-build-0.4224 | pl526_3 126 KB bioconda perl-text-abbrev-1.02 | pl526_0 5 KB bioconda perl-text-parsewords-3.30 | pl526_0 8 KB bioconda prodigal-2.6.3 | h516909a_2 777 KB bioconda r-assertthat-0.2.1 | r36h6115d3f_2 70 KB conda-forge r-backports-1.1.6 | r36hcdcec82_2 77 KB conda-forge r-base-3.6.0 | hce969dd_0 39.4 MB r-callr-3.4.3 | r36h6115d3f_1 392 KB conda-forge r-cli-2.0.2 | r36h6115d3f_1 395 KB conda-forge r-colorspace-1.4_1 | r36hcdcec82_2 2.4 MB conda-forge r-crayon-1.3.4 | r36h6115d3f_1003 747 KB conda-forge r-desc-1.2.0 | r36h6115d3f_1003 290 KB conda-forge r-digest-0.6.25 | r36h0357c0b_2 199 KB conda-forge r-ellipsis-0.3.0 | r36hcdcec82_1 47 KB conda-forge r-evaluate-0.14 | r36h6115d3f_2 81 KB conda-forge r-fansi-0.4.1 | r36hcdcec82_1 196 KB conda-forge r-farver-2.0.3 | r36h0357c0b_1 1.4 MB conda-forge r-ggplot2-3.3.0 | r36h6115d3f_1 3.9 MB conda-forge r-glue-1.4.0 | r36hcdcec82_1 144 KB conda-forge r-gtable-0.3.0 | r36h6115d3f_3 423 KB conda-forge r-isoband-0.2.1 | r36h0357c0b_1 2.5 MB conda-forge r-labeling-0.3 | r36h6115d3f_1003 67 KB conda-forge r-lattice-0.20_41 | r36hcdcec82_2 1.1 MB conda-forge r-lifecycle-0.2.0 | r36h6115d3f_1 112 KB conda-forge r-magrittr-1.5 | r36h6115d3f_1003 167 KB conda-forge r-mass-7.3_51.6 | r36hcdcec82_2 1.1 MB conda-forge r-matrix-1.2_18 | r36hcdcec82_0 3.8 MB conda-forge r-mgcv-1.8_31 | r36hcdcec82_0 2.7 MB conda-forge r-munsell-0.5.0 | r36h6115d3f_1003 246 KB conda-forge r-nlme-3.1_147 | r36h9bbef5b_1 2.3 MB conda-forge r-pillar-1.4.4 | r36h6115d3f_0 197 KB conda-forge r-pkgbuild-1.0.8 | r36h6115d3f_0 153 KB conda-forge r-pkgconfig-2.0.3 | r36h6115d3f_1 24 KB conda-forge r-pkgload-1.0.2 | r36h0357c0b_1002 162 KB conda-forge r-praise-1.0.0 | r36h6115d3f_1004 23 KB conda-forge r-prettyunits-1.1.1 | r36h6115d3f_1 41 KB conda-forge r-processx-3.4.2 | r36hcdcec82_1 271 KB conda-forge r-ps-1.3.3 | r36hcdcec82_0 235 KB conda-forge r-r6-2.4.1 | r36h6115d3f_1 63 KB conda-forge r-rcolorbrewer-1.1_2 | r36h6115d3f_1003 59 KB conda-forge r-rcpp-1.0.4.6 | r36h0357c0b_1 1.9 MB conda-forge r-rlang-0.4.6 | r36hcdcec82_0 1.0 MB conda-forge r-rprojroot-1.3_2 | r36h6115d3f_1003 94 KB conda-forge r-rstudioapi-0.11 | r36h6115d3f_1 267 KB conda-forge r-scales-1.1.1 | r36h6115d3f_0 558 KB conda-forge r-testthat-2.3.2 | r36h0357c0b_1 1.1 MB conda-forge r-tibble-3.0.1 | r36hcdcec82_1 382 KB conda-forge r-utf8-1.1.4 | r36hcdcec82_1003 161 KB conda-forge r-vctrs-0.3.0 | r36hcdcec82_0 959 KB conda-forge r-viridislite-0.3.0 | r36h6115d3f_1003 64 KB conda-forge r-withr-2.2.0 | r36h6115d3f_1 227 KB conda-forge r-zeallot-0.1.0 | r36h6115d3f_1002 62 KB conda-forge sepp-4.3.10 | py37_0 6.6 MB bioconda suitesparse-5.2.0 | h9e4a6bb_0 2.4 MB tktable-2.10 | h14c3975_0 88 KB ------------------------------------------------------------ Total: 389.5 MB The following NEW packages will be INSTALLED: _r-mutex conda-forge/noarch::_r-mutex-1.0.1-anacondar_1 augustus bioconda/linux-64::augustus-3.2.3-pl526hcfae127_5 bamtools bioconda/linux-64::bamtools-2.4.1-1 binutils_impl_lin~ conda-forge/linux-64::binutils_impl_linux-64-2.34-h53a641e_0 binutils_linux-64 conda-forge/linux-64::binutils_linux-64-2.34-hc952b39_18 biopython conda-forge/linux-64::biopython-1.76-py37h516909a_0 blast bioconda/linux-64::blast-2.2.31-1 busco bioconda/noarch::busco-4.0.6-pyr36_0 bwidget conda-forge/linux-64::bwidget-1.9.14-0 dendropy bioconda/noarch::dendropy-4.4.0-py_1 findutils conda-forge/linux-64::findutils-4.6.0-h14c3975_1000 gcc_impl_linux-64 pkgs/main/linux-64::gcc_impl_linux-64-7.3.0-habb00fd_1 gcc_linux-64 conda-forge/linux-64::gcc_linux-64-7.3.0-h553295d_18 gettext conda-forge/linux-64::gettext-0.19.8.1-hc5be6a0_1002 gfortran_impl_lin~ conda-forge/linux-64::gfortran_impl_linux-64-7.3.0-hdf63c60_5 gfortran_linux-64 conda-forge/linux-64::gfortran_linux-64-7.3.0-h553295d_18 gsl pkgs/main/linux-64::gsl-2.2.1-h0c605f7_3 gxx_impl_linux-64 pkgs/main/linux-64::gxx_impl_linux-64-7.3.0-hdf63c60_1 gxx_linux-64 conda-forge/linux-64::gxx_linux-64-7.3.0-h553295d_18 hmmer bioconda/linux-64::hmmer-3.1b2-3 ld_impl_linux-64 conda-forge/linux-64::ld_impl_linux-64-2.34-h53a641e_0 libgfortran conda-forge/linux-64::libgfortran-3.0.0-1 lp_solve conda-forge/linux-64::lp_solve-5.5.2.5-h14c3975_1001 make conda-forge/linux-64::make-4.3-h516909a_0 metis conda-forge/linux-64::metis-5.1.0-he1b5a44_1005 openblas conda-forge/linux-64::openblas-0.2.20-8 perl-app-cpanminus bioconda/linux-64::perl-app-cpanminus-1.7044-pl526_1 perl-carp bioconda/linux-64::perl-carp-1.38-pl526_3 perl-constant bioconda/linux-64::perl-constant-1.33-pl526_1 perl-cpan-meta bioconda/linux-64::perl-cpan-meta-2.150010-pl526_0 perl-cpan-meta-re~ bioconda/linux-64::perl-cpan-meta-requirements-2.140-pl526_0 perl-cpan-meta-ya~ bioconda/linux-64::perl-cpan-meta-yaml-0.018-pl526_0 perl-data-dumper bioconda/linux-64::perl-data-dumper-2.173-pl526_0 perl-dbi bioconda/linux-64::perl-dbi-1.642-pl526_0 perl-encode bioconda/linux-64::perl-encode-2.88-pl526_1 perl-exporter bioconda/linux-64::perl-exporter-5.72-pl526_1 perl-extutils-cbu~ bioconda/linux-64::perl-extutils-cbuilder-0.280230-pl526_1 perl-extutils-mak~ bioconda/linux-64::perl-extutils-makemaker-7.36-pl526_1 perl-extutils-man~ bioconda/linux-64::perl-extutils-manifest-1.72-pl526_0 perl-extutils-par~ bioconda/linux-64::perl-extutils-parsexs-3.35-pl526_0 perl-file-path bioconda/linux-64::perl-file-path-2.16-pl526_0 perl-file-temp bioconda/linux-64::perl-file-temp-0.2304-pl526_2 perl-getopt-long bioconda/linux-64::perl-getopt-long-2.50-pl526_1 perl-ipc-cmd bioconda/linux-64::perl-ipc-cmd-1.02-pl526_0 perl-json-pp bioconda/noarch::perl-json-pp-4.04-pl526_0 perl-locale-maket~ bioconda/linux-64::perl-locale-maketext-simple-0.21-pl526_2 perl-module-build bioconda/linux-64::perl-module-build-0.4224-pl526_3 perl-module-corel~ bioconda/linux-64::perl-module-corelist-5.20190524-pl526_0 perl-module-load bioconda/linux-64::perl-module-load-0.32-pl526_1 perl-module-load-~ bioconda/linux-64::perl-module-load-conditional-0.68-pl526_2 perl-module-metad~ bioconda/linux-64::perl-module-metadata-1.000036-pl526_0 perl-params-check bioconda/linux-64::perl-params-check-0.38-pl526_1 perl-parent bioconda/linux-64::perl-parent-0.236-pl526_1 perl-perl-ostype bioconda/linux-64::perl-perl-ostype-1.010-pl526_1 perl-scalar-list-~ bioconda/linux-64::perl-scalar-list-utils-1.52-pl526h516909a_0 perl-text-abbrev bioconda/linux-64::perl-text-abbrev-1.02-pl526_0 perl-text-parsewo~ bioconda/linux-64::perl-text-parsewords-3.30-pl526_0 perl-version bioconda/linux-64::perl-version-0.9924-pl526_0 perl-yaml bioconda/noarch::perl-yaml-1.29-pl526_0 prodigal bioconda/linux-64::prodigal-2.6.3-h516909a_2 r-assertthat conda-forge/noarch::r-assertthat-0.2.1-r36h6115d3f_2 r-backports conda-forge/linux-64::r-backports-1.1.6-r36hcdcec82_2 r-base pkgs/r/linux-64::r-base-3.6.0-hce969dd_0 r-callr conda-forge/noarch::r-callr-3.4.3-r36h6115d3f_1 r-cli conda-forge/noarch::r-cli-2.0.2-r36h6115d3f_1 r-colorspace conda-forge/linux-64::r-colorspace-1.4_1-r36hcdcec82_2 r-crayon conda-forge/noarch::r-crayon-1.3.4-r36h6115d3f_1003 r-desc conda-forge/noarch::r-desc-1.2.0-r36h6115d3f_1003 r-digest conda-forge/linux-64::r-digest-0.6.25-r36h0357c0b_2 r-ellipsis conda-forge/linux-64::r-ellipsis-0.3.0-r36hcdcec82_1 r-evaluate conda-forge/noarch::r-evaluate-0.14-r36h6115d3f_2 r-fansi conda-forge/linux-64::r-fansi-0.4.1-r36hcdcec82_1 r-farver conda-forge/linux-64::r-farver-2.0.3-r36h0357c0b_1 r-ggplot2 conda-forge/noarch::r-ggplot2-3.3.0-r36h6115d3f_1 r-glue conda-forge/linux-64::r-glue-1.4.0-r36hcdcec82_1 r-gtable conda-forge/noarch::r-gtable-0.3.0-r36h6115d3f_3 r-isoband conda-forge/linux-64::r-isoband-0.2.1-r36h0357c0b_1 r-labeling conda-forge/noarch::r-labeling-0.3-r36h6115d3f_1003 r-lattice conda-forge/linux-64::r-lattice-0.20_41-r36hcdcec82_2 r-lifecycle conda-forge/noarch::r-lifecycle-0.2.0-r36h6115d3f_1 r-magrittr conda-forge/noarch::r-magrittr-1.5-r36h6115d3f_1003 r-mass conda-forge/linux-64::r-mass-7.3_51.6-r36hcdcec82_2 r-matrix conda-forge/linux-64::r-matrix-1.2_18-r36hcdcec82_0 r-mgcv conda-forge/linux-64::r-mgcv-1.8_31-r36hcdcec82_0 r-munsell conda-forge/noarch::r-munsell-0.5.0-r36h6115d3f_1003 r-nlme conda-forge/linux-64::r-nlme-3.1_147-r36h9bbef5b_1 r-pillar conda-forge/noarch::r-pillar-1.4.4-r36h6115d3f_0 r-pkgbuild conda-forge/noarch::r-pkgbuild-1.0.8-r36h6115d3f_0 r-pkgconfig conda-forge/noarch::r-pkgconfig-2.0.3-r36h6115d3f_1 r-pkgload conda-forge/linux-64::r-pkgload-1.0.2-r36h0357c0b_1002 r-praise conda-forge/noarch::r-praise-1.0.0-r36h6115d3f_1004 r-prettyunits conda-forge/noarch::r-prettyunits-1.1.1-r36h6115d3f_1 r-processx conda-forge/linux-64::r-processx-3.4.2-r36hcdcec82_1 r-ps conda-forge/linux-64::r-ps-1.3.3-r36hcdcec82_0 r-r6 conda-forge/noarch::r-r6-2.4.1-r36h6115d3f_1 r-rcolorbrewer conda-forge/noarch::r-rcolorbrewer-1.1_2-r36h6115d3f_1003 r-rcpp conda-forge/linux-64::r-rcpp-1.0.4.6-r36h0357c0b_1 r-rlang conda-forge/linux-64::r-rlang-0.4.6-r36hcdcec82_0 r-rprojroot conda-forge/noarch::r-rprojroot-1.3_2-r36h6115d3f_1003 r-rstudioapi conda-forge/noarch::r-rstudioapi-0.11-r36h6115d3f_1 r-scales conda-forge/noarch::r-scales-1.1.1-r36h6115d3f_0 r-testthat conda-forge/linux-64::r-testthat-2.3.2-r36h0357c0b_1 r-tibble conda-forge/linux-64::r-tibble-3.0.1-r36hcdcec82_1 r-utf8 conda-forge/linux-64::r-utf8-1.1.4-r36hcdcec82_1003 r-vctrs conda-forge/linux-64::r-vctrs-0.3.0-r36hcdcec82_0 r-viridislite conda-forge/noarch::r-viridislite-0.3.0-r36h6115d3f_1003 r-withr conda-forge/noarch::r-withr-2.2.0-r36h6115d3f_1 r-zeallot conda-forge/noarch::r-zeallot-0.1.0-r36h6115d3f_1002 sepp bioconda/linux-64::sepp-4.3.10-py37_0 suitesparse pkgs/main/linux-64::suitesparse-5.2.0-h9e4a6bb_0 tktable pkgs/main/linux-64::tktable-2.10-h14c3975_0 The following packages will be UPDATED: libpng pkgs/main::libpng-1.6.36-hbc83047_0 --> conda-forge::libpng-1.6.37-hed695b0_1 libssh2 pkgs/main::libssh2-1.8.0-h1ba5d50_4 --> conda-forge::libssh2-1.9.0-hab1572f_1 The following packages will be SUPERSEDED by a higher-priority channel: certifi pkgs/main::certifi-2020.4.5.1-py37_0 --> conda-forge::certifi-2020.4.5.1-py37hc8dfbb8_0 Proceed ([y]/n)? y]]> Jit https://bioinformaticsonline.com/snippets/view/41601/install-kraken-on-linux Mon, 04 May 2020 04:16:39 -0500 https://bioinformaticsonline.com/snippets/view/41601/install-kraken-on-linux $ conda install -c bioconda kraken Collecting package metadata (repodata.json): done Solving environment: done ## Package Plan ## environment location: /home/anaconda3 added / updated specs: - kraken The following packages will be downloaded: package | build ---------------------------|----------------- jellyfish-1.1.12 | h6bb024c_1 3.1 MB bioconda kraken-1.1 | h470a237_2 114 KB bioconda ------------------------------------------------------------ Total: 3.2 MB The following NEW packages will be INSTALLED: jellyfish bioconda/linux-64::jellyfish-1.1.12-h6bb024c_1 kraken bioconda/linux-64::kraken-1.1-h470a237_2 perl pkgs/main/linux-64::perl-5.26.2-h14c3975_0 Proceed ([y]/n)? y Downloading and Extracting Packages kraken-1.1 | 114 KB | ################################################## | 100% jellyfish-1.1.12 | 3.1 MB | ################################################## | 100% Preparing transaction: done Verifying transaction: done Executing transaction: done $conda install -c bioconda kraken-all Collecting package metadata (repodata.json): done Solving environment: done ## Package Plan ## environment location: /home/anaconda3 added / updated specs: - kraken-all The following packages will be downloaded: package | build ---------------------------|----------------- kraken-0.10.6_eaf8fb68 | 2 98 KB bioconda kraken-all-0.10.6_eaf8fb68 | 0 857 B bioconda perl-threaded-5.26.0 | 0 4 KB bioconda ------------------------------------------------------------ Total: 103 KB The following NEW packages will be INSTALLED: kraken-all bioconda/linux-64::kraken-all-0.10.6_eaf8fb68-0 perl-threaded bioconda/linux-64::perl-threaded-5.26.0-0 The following packages will be SUPERSEDED by a higher-priority channel: kraken bioconda/label/cf201901::kraken-1.1-h~ --> bioconda::kraken-0.10.6_eaf8fb68-2 Proceed ([y]/n)? y Downloading and Extracting Packages kraken-0.10.6_eaf8fb | 98 KB | ################################################## | 100% kraken-all-0.10.6_ea | 857 B | ################################################## | 100% perl-threaded-5.26.0 | 4 KB | ################################################## | 100% Preparing transaction: done Verifying transaction: done Executing transaction: done]]> Shruti Paniwala https://bioinformaticsonline.com/snippets/view/41596/install-ragout-genome-assembler Sat, 02 May 2020 06:46:00 -0500 https://bioinformaticsonline.com/snippets/view/41596/install-ragout-genome-assembler $ conda install -c bioconda ragout Collecting package metadata (repodata.json): done Solving environment: done ## Package Plan ## environment location: /home/anaconda3 added / updated specs: - ragout The following packages will be downloaded: package | build ---------------------------|----------------- decorator-4.3.0 | py37_0 15 KB ragout-2.3 | py37hc9558a2_0 2.8 MB bioconda sibelia-3.0.7 | he1b5a44_2 24.8 MB bioconda ------------------------------------------------------------ Total: 27.6 MB The following NEW packages will be INSTALLED: ragout bioconda/linux-64::ragout-2.3-py37hc9558a2_0 sibelia bioconda/linux-64::sibelia-3.0.7-he1b5a44_2 The following packages will be DOWNGRADED: decorator 4.4.0-py37_1 --> 4.3.0-py37_0 Proceed ([y]/n)? y Downloading and Extracting Packages ragout-2.3 | 2.8 MB | ################################################## | 100% sibelia-3.0.7 | 24.8 MB | ################################################## | 100% decorator-4.3.0 | 15 KB | ################################################## | 100% Preparing transaction: done Verifying transaction: done Executing transaction: done]]> Neel https://bioinformaticsonline.com/snippets/view/41481/check-os-version-in-linux Fri, 20 Mar 2020 06:28:14 -0500 https://bioinformaticsonline.com/snippets/view/41481/check-os-version-in-linux The procedure to find os name and version on Linux: #Open the terminal application (bash shell) #For remote server login using the ssh: ssh user@server-name #Type any one of the following command to find os name and version in Linux: cat /etc/os-release lsb_release -a hostnamectl #Type the following command to find Linux kernel version: uname -r]]> Radha Agarkar https://bioinformaticsonline.com/snippets/view/41470/basic-docker-commands Wed, 18 Mar 2020 07:33:03 -0500 https://bioinformaticsonline.com/snippets/view/41470/basic-docker-commands jit@jit-HP-Pro-3335-MT:~/Downloads/testDock$ sudo docker system df TYPE TOTAL ACTIVE SIZE RECLAIMABLE Images 47 39 3.701GB 3.177GB (85%) Containers 121 0 1.513GB 1.513GB (100%) Local Volumes 0 0 0B 0B Build Cache 0 0 0B 0B jit@jit-HP-Pro-3335-MT:~/Downloads/testDock$ sudo docker system prune WARNING! This will remove: - all stopped containers - all networks not used by at least one container - all dangling images - all dangling build cache Are you sure you want to continue? [y/N] y Deleted Containers: 0b523b97fd6d70456bad5843147ec3f5c069c20cc1d7048ce78202058b63b2a6 9d6d29988baa09b2f1a1745de448896d2820ba52f9927497d5a1d433cb01c61a 5baf6ec5bb11291090b386ad85574a64db7bbb7a01d504e6d6174a80e05628bb Deleted Images: deleted: sha256:a62df23989f7419cfb04d9fee7fee8c6dcf548bbb0af6a63bd02d5629f2189f8 deleted: sha256:d8c4b90ecbd8d3ad6a09a34c5880d9d68233ec2e5760a630684e1012eaf4ded6 deleted: sha256:85a4247b883f9cc31cb59e93f135d243837190bcd010b626604895fa8f20dcec Total reclaimed space: 2.049GB jit@jit-HP-Pro-3335-MT:~/Downloads/testDock$ sudo docker system df TYPE TOTAL ACTIVE SIZE RECLAIMABLE Images 9 0 3.165GB 3.165GB (100%) Containers 0 0 0B 0B Local Volumes 0 0 0B 0B Build Cache 0 0 0B 0B jit@jit-HP-Pro-3335-MT:~/Downloads/testDock$ sudo docker build -t mydocker . Sending build context to Docker daemon 9.023MB Step 1/12 : FROM ubuntu:14.04 ---> 6e4f1fe62ff1 Step 2/12 : FROM perl:latest ---> 82330051f9cb Step 3/12 : FROM bioperl/bioperl-deps ---> e890cc223da3 Step 4/12 : MAINTAINER "Jitendra Narayan" <jnarayan81@gmail.com> ---> Using cache ---> 13519702cbe1 Step 5/12 : RUN apt-get update --yes && apt-get install --yes git ---> Using cache ---> 0974217c0b0e Step 6/12 : RUN apt-get install --yes build-essential gcc-multilib perl ---> Using cache ---> 96d284c0408b Step 7/12 : RUN apt-get install -y bioperl && apt-get install -y libstatistics-distributions-perl && apt-get install -y libterm-progressbar-simple-perl && apt-get install -y libbio-scf-perl ---> Using cache ---> 3509d5eb05a5 Step 8/12 : RUN apt-get install -y curl && cpan install App::cpanminus ---> Using cache ---> e79748ebdffd Step 9/12 : RUN cpanm install File::chdir && cpanm install lib::abs && cpanm install File::Remove && cpanm install Spreadsheet::Read && cpanm install Statistics::ChiSquare ---> Using cache ---> d34787da52e0 Step 10/12 : WORKDIR home/ ---> Using cache ---> d1ba7714283f Step 11/12 : COPY autoConTAMPR home/ ---> Using cache ---> cc3fe61a6e14 Step 12/12 : ENTRYPOINT ["perl", "home/bin/autoConTAMPR.pl"] ---> Using cache ---> 4a2cc5876794 Successfully built 4a2cc5876794 Successfully tagged mydocker:latest jit@jit-HP-Pro-3335-MT:~/Downloads/testDock$ sudo docker run mydocker --.---. .-. .--- / \ / ^ \ --autoConTAMPR v0.1-- Citation - autoConTAMPR: Automatic Contingency Table Analysis of Minority Peak Ranks License: Creative Commons Licence Bug-reports and requests to: https://github.com/jnarayan81/autoConTAMPR/issues Operating system: linux Perl executable at: /usr/bin/perl Please check manual. Usage: autoConTAMPR.pl --validate/-v autoConTAMPR.pl --validate/-v --conf/-c <configuration file> autoConTAMPR.pl --plot/-p autoConTAMPR.pl --plot/-p --conf/-c <configuration file> autoConTAMPR.pl --install/-i autoConTAMPR.pl --install/-i --conf/-c <configuration file> jit@jit-HP-Pro-3335-MT:~/Downloads/testDock$ sudo docker system info Client: Debug Mode: false Server: Containers: 1 Running: 0 Paused: 0 Stopped: 1 Images: 17 Server Version: 19.03.8 Storage Driver: overlay2 Backing Filesystem: <unknown> Supports d_type: true Native Overlay Diff: true Logging Driver: json-file Cgroup Driver: cgroupfs Plugins: Volume: local Network: bridge host ipvlan macvlan null overlay Log: awslogs fluentd gcplogs gelf journald json-file local logentries splunk syslog Swarm: inactive Runtimes: runc Default Runtime: runc Init Binary: docker-init init version: fec3683 Security Options: apparmor seccomp Profile: default Kernel Version: 4.15.0-88-generic Operating System: Ubuntu 18.04.4 LTS OSType: linux Architecture: x86_64 CPUs: 2 Total Memory: 3.594GiB Name: jit-HP-Pro-3335-MTL Docker Root Dir: /var/lib/docker Debug Mode: false Registry: https://index.docker.io/v1/ Labels: Experimental: false Insecure Registries: 127.0.0.0/8 Live Restore Enabled: false WARNING: No swap limit support]]> Jit https://bioinformaticsonline.com/snippets/view/41450/commands-to-install-statisticsr-module-in-ubuntu Mon, 16 Mar 2020 06:59:18 -0500 https://bioinformaticsonline.com/snippets/view/41450/commands-to-install-statisticsr-module-in-ubuntu $ sudo apt-get install libstatistics-r-perl Reading package lists... Done Building dependency tree Reading state information... Done The following additional packages will be installed: r-base r-base-html Suggested packages: ess r-doc-info | r-doc-pdf The following NEW packages will be installed: libstatistics-r-perl r-base r-base-html 0 upgraded, 3 newly installed, 0 to remove and 0 not upgraded. Need to get 87.4 kB of archives. After this operation, 706 kB of additional disk space will be used. Do you want to continue? [Y/n] Y\ Get:1 http://in.archive.ubuntu.com/ubuntu bionic/universe amd64 r-base all 3.4.4-1ubuntu1 [9,312 B] Get:2 http://in.archive.ubuntu.com/ubuntu bionic/universe amd64 libstatistics-r-perl all 0.24-1 [23.3 kB] Get:3 http://in.archive.ubuntu.com/ubuntu bionic/universe amd64 r-base-html all 3.4.4-1ubuntu1 [54.8 kB] Fetched 87.4 kB in 1s (84.0 kB/s) Selecting previously unselected package r-base. (Reading database ... 209534 files and directories currently installed.) Preparing to unpack .../r-base_3.4.4-1ubuntu1_all.deb ... Unpacking r-base (3.4.4-1ubuntu1) ... Selecting previously unselected package libstatistics-r-perl. Preparing to unpack .../libstatistics-r-perl_0.24-1_all.deb ... Unpacking libstatistics-r-perl (0.24-1) ... Selecting previously unselected package r-base-html. Preparing to unpack .../r-base-html_3.4.4-1ubuntu1_all.deb ... Unpacking r-base-html (3.4.4-1ubuntu1) ... Setting up r-base-html (3.4.4-1ubuntu1) ... Setting up r-base (3.4.4-1ubuntu1) ... Setting up libstatistics-r-perl (0.24-1) ... Processing triggers for man-db (2.8.3-2ubuntu0.1) ...]]> Jit https://bioinformaticsonline.com/snippets/view/41447/commands-to-install-conda-in-ubuntu Mon, 16 Mar 2020 04:11:01 -0500 https://bioinformaticsonline.com/snippets/view/41447/commands-to-install-conda-in-ubuntu jit@jit-HP-Pro-3335-MT:~/Downloads$ mkdir jittmp jit@jit-HP-Pro-3335-MT:~/Downloads$ cd jittmp/ jit@jit-HP-Pro-3335-MT:~/Downloads/jittmp$ curl -O https://repo.anaconda.com/archive/Anaconda3-2019.03-Linux-x86_64.sh % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 100 654M 100 654M 0 0 33.6M 0 0:00:19 0:00:19 --:--:-- 33.2M jit@jit-HP-Pro-3335-MT:~/Downloads/jittmp$ sha256sum Anaconda3-2019.03-Linux-x86_64.sh 45c851b7497cc14d5ca060064394569f724b67d9b5f98a926ed49b834a6bb73a Anaconda3-2019.03-Linux-x86_64.sh jit@jit-HP-Pro-3335-MT:~/Downloads/jittmp$ bash Anaconda3-2019.03-Linux-x86_64.sh Welcome to Anaconda3 2019.03 In order to continue the installation process, please review the license agreement. Please, press ENTER to continue >>> =================================== Anaconda End User License Agreement =================================== Copyright 2015, Anaconda, Inc. All rights reserved under the 3-clause BSD License: Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, th is list of conditions and the following disclaimer in the documentation and/or o ther materials provided with the distribution. * Neither the name of Anaconda, Inc. ("Anaconda, Inc.") nor the names of its c ontributors may be used to endorse or promote products derived from this softwar e without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WA RRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL ANACONDA, INC. BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL , SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, P ROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BU SINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN C ONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING I N ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. Notice of Third Party Software Licenses ======================================= Anaconda Distribution contains open source software packages from third parties. These are available on an "as is" basis and subject to their individual license agreements. These licenses are available in Anaconda Distribution or at http:// docs.anaconda.com/anaconda/pkg-docs. Any binary packages of these third party to ols you obtain via Anaconda Distribution are subject to their individual license s as well as the Anaconda license. Anaconda, Inc. reserves the right to change w hich third party tools are provided in Anaconda Distribution. In particular, Anaconda Distribution contains re-distributable, run-time, shared -library files from the Intel(TM) Math Kernel Library ("MKL binaries"). You are specifically authorized to use the MKL binaries with your installation of Anacon da Distribution. You are also authorized to redistribute the MKL binaries with A naconda Distribution or in the conda package that contains them. Use and redistr ibution of the MKL binaries are subject to the licensing terms located at https: //software.intel.com/en-us/license/intel-simplified-software-license. If needed, instructions for removing the MKL binaries after installation of Anaconda Distr ibution are available at http://www.anaconda.com. Anaconda Distribution also contains cuDNN software binaries from NVIDIA Corporat ion ("cuDNN binaries"). You are specifically authorized to use the cuDNN binarie s with your installation of Anaconda Distribution. You are also authorized to re distribute the cuDNN binaries with an Anaconda Distribution package that contain s them. If needed, instructions for removing the cuDNN binaries after installati on of Anaconda Distribution are available at http://www.anaconda.com. Anaconda Distribution also contains Visual Studio Code software binaries from Mi crosoft Corporation ("VS Code"). You are specifically authorized to use VS Code with your installation of Anaconda Distribution. Use of VS Code is subject to th e licensing terms located at https://code.visualstudio.com/License. Cryptography Notice =================== This distribution includes cryptographic software. The country in which you curr ently reside may have restrictions on the import, possession, use, and/or re-exp ort to another country, of encryption software. BEFORE using any encryption soft ware, please check your country's laws, regulations and policies concerning the import, possession, or use, and re-export of encryption software, to see if this is permitted. See the Wassenaar Arrangement http://www.wassenaar.org/ for more information. Anaconda, Inc. has self-classified this software as Export Commodity Control Num ber (ECCN) 5D992b, which includes mass market information security software usin g or performing cryptographic functions with asymmetric algorithms. No license i s required for export of this software to non-embargoed countries. In addition, the Intel(TM) Math Kernel Library contained in Anaconda, Inc.'s software is clas sified by Intel(TM) as ECCN 5D992b with no license required for export to non-em bargoed countries and Microsoft's Visual Studio Code software is classified by M icrosoft as ECCN 5D992.c with no license required for export to non-embargoed co untries. The following packages are included in this distribution that relate to cryptogr aphy: openssl The OpenSSL Project is a collaborative effort to develop a robust, commercia l-grade, full-featured, and Open Source toolkit implementing the Transport Layer Security (TLS) and Secure Sockets Layer (SSL) protocols as well as a full-stren gth general purpose cryptography library. pycrypto A collection of both secure hash functions (such as SHA256 and RIPEMD160), a nd various encryption algorithms (AES, DES, RSA, ElGamal, etc.). pyopenssl A thin Python wrapper around (a subset of) the OpenSSL library. kerberos (krb5, non-Windows platforms) A network authentication protocol designed to provide strong authentication for client/server applications by using secret-key cryptography. cryptography A Python library which exposes cryptographic recipes and primitives. Do you accept the license terms? [yes|no] Please answer 'yes' or 'no':' >>> yes Anaconda3 will now be installed into this location: /home/jit/anaconda3 - Press ENTER to confirm the location - Press CTRL-C to abort the installation - Or specify a different location below [/home/jit/anaconda3] >>> PREFIX=/home/jit/anaconda3 installing: python-3.7.3-h0371630_0 ... Python 3.7.3 installing: conda-env-2.6.0-1 ... installing: blas-1.0-mkl ... installing: ca-certificates-2019.1.23-0 ... installing: intel-openmp-2019.3-199 ... installing: libgcc-ng-8.2.0-hdf63c60_1 ... installing: libgfortran-ng-7.3.0-hdf63c60_0 ... installing: libstdcxx-ng-8.2.0-hdf63c60_1 ... installing: bzip2-1.0.6-h14c3975_5 ... installing: expat-2.2.6-he6710b0_0 ... installing: fribidi-1.0.5-h7b6447c_0 ... installing: gmp-6.1.2-h6c8ec71_1 ... installing: graphite2-1.3.13-h23475e2_0 ... installing: icu-58.2-h9c2bf20_1 ... installing: jbig-2.1-hdba287a_0 ... installing: jpeg-9b-h024ee3a_2 ... installing: libffi-3.2.1-hd88cf55_4 ... installing: liblief-0.9.0-h7725739_2 ... installing: libsodium-1.0.16-h1bed415_0 ... installing: libtool-2.4.6-h7b6447c_5 ... installing: libuuid-1.0.3-h1bed415_2 ... installing: libxcb-1.13-h1bed415_1 ... installing: lz4-c-1.8.1.2-h14c3975_0 ... installing: lzo-2.10-h49e0be7_2 ... installing: mkl-2019.3-199 ... installing: ncurses-6.1-he6710b0_1 ... installing: openssl-1.1.1b-h7b6447c_1 ... installing: patchelf-0.9-he6710b0_3 ... installing: pcre-8.43-he6710b0_0 ... installing: pixman-0.38.0-h7b6447c_0 ... installing: snappy-1.1.7-hbae5bb6_3 ... installing: xz-5.2.4-h14c3975_4 ... installing: yaml-0.1.7-had09818_2 ... installing: zlib-1.2.11-h7b6447c_3 ... installing: blosc-1.15.0-hd408876_0 ... installing: glib-2.56.2-hd408876_0 ... installing: hdf5-1.10.4-hb1b8bf9_0 ... installing: libedit-3.1.20181209-hc058e9b_0 ... installing: libpng-1.6.36-hbc83047_0 ... installing: libssh2-1.8.0-h1ba5d50_4 ... installing: libxml2-2.9.9-he19cac6_0 ... installing: mpfr-4.0.1-hdf1c602_3 ... installing: pandoc-2.2.3.2-0 ... installing: readline-7.0-h7b6447c_5 ... installing: tk-8.6.8-hbc83047_0 ... installing: zeromq-4.3.1-he6710b0_3 ... installing: zstd-1.3.7-h0b5b093_0 ... installing: dbus-1.13.6-h746ee38_0 ... installing: freetype-2.9.1-h8a8886c_1 ... installing: gstreamer-1.14.0-hb453b48_1 ... installing: krb5-1.16.1-h173b8e3_7 ... installing: libarchive-3.3.3-h5d8350f_5 ... installing: libtiff-4.0.10-h2733197_2 ... installing: libxslt-1.1.33-h7d1a2b0_0 ... installing: mpc-1.1.0-h10f8cd9_1 ... installing: sqlite-3.27.2-h7b6447c_0 ... installing: unixodbc-2.3.7-h14c3975_0 ... installing: fontconfig-2.13.0-h9420a91_0 ... installing: gst-plugins-base-1.14.0-hbbd80ab_1 ... installing: libcurl-7.64.0-h20c2e04_2 ... installing: alabaster-0.7.12-py37_0 ... installing: asn1crypto-0.24.0-py37_0 ... installing: atomicwrites-1.3.0-py37_1 ... installing: attrs-19.1.0-py37_1 ... installing: backcall-0.1.0-py37_0 ... installing: backports-1.0-py37_1 ... installing: bitarray-0.8.3-py37h14c3975_0 ... installing: boto-2.49.0-py37_0 ... installing: cairo-1.14.12-h8948797_3 ... installing: certifi-2019.3.9-py37_0 ... installing: chardet-3.0.4-py37_1 ... installing: click-7.0-py37_0 ... installing: cloudpickle-0.8.0-py37_0 ... installing: colorama-0.4.1-py37_0 ... installing: contextlib2-0.5.5-py37_0 ... installing: curl-7.64.0-hbc83047_2 ... installing: dask-core-1.1.4-py37_1 ... installing: decorator-4.4.0-py37_1 ... installing: defusedxml-0.5.0-py37_1 ... installing: docutils-0.14-py37_0 ... installing: entrypoints-0.3-py37_0 ... installing: et_xmlfile-1.0.1-py37_0 ... installing: fastcache-1.0.2-py37h14c3975_2 ... installing: filelock-3.0.10-py37_0 ... installing: future-0.17.1-py37_0 ... installing: glob2-0.6-py37_1 ... installing: gmpy2-2.0.8-py37h10f8cd9_2 ... installing: greenlet-0.4.15-py37h7b6447c_0 ... installing: heapdict-1.0.0-py37_2 ... installing: idna-2.8-py37_0 ... installing: imagesize-1.1.0-py37_0 ... installing: ipython_genutils-0.2.0-py37_0 ... installing: itsdangerous-1.1.0-py37_0 ... installing: jdcal-1.4-py37_0 ... installing: jeepney-0.4-py37_0 ... installing: kiwisolver-1.0.1-py37hf484d3e_0 ... installing: lazy-object-proxy-1.3.1-py37h14c3975_2 ... installing: llvmlite-0.28.0-py37hd408876_0 ... installing: locket-0.2.0-py37_1 ... installing: lxml-4.3.2-py37hefd8a0e_0 ... 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Do you wish the installer to initialize Anaconda3 by running conda init? [yes|no] [no] >>> yes WARNING: The conda.compat module is deprecated and will be removed in a future release. no change /home/jit/anaconda3/condabin/conda no change /home/jit/anaconda3/bin/conda no change /home/jit/anaconda3/bin/conda-env no change /home/jit/anaconda3/bin/activate no change /home/jit/anaconda3/bin/deactivate no change /home/jit/anaconda3/etc/profile.d/conda.sh no change /home/jit/anaconda3/etc/fish/conf.d/conda.fish no change /home/jit/anaconda3/shell/condabin/Conda.psm1 no change /home/jit/anaconda3/shell/condabin/conda-hook.ps1 no change /home/jit/anaconda3/lib/python3.7/site-packages/xonsh/conda.xsh no change /home/jit/anaconda3/etc/profile.d/conda.csh modified /home/jit/.bashrc ==> For changes to take effect, close and re-open your current shell. <== If you'd prefer that conda's base environment not be activated on startup, set the auto_activate_base parameter to false: conda config --set auto_activate_base false Thank you for installing Anaconda3! =========================================================================== Anaconda and JetBrains are working together to bring you Anaconda-powered environments tightly integrated in the PyCharm IDE. PyCharm for Anaconda is available at: https://www.anaconda.com/pycharm]]> Jit