https://bioinformaticsonline.com/snippets?offset=190 https://bioinformaticsonline.com/snippets/view/42563/install-asciigenome-using-conda Wed, 06 Jan 2021 05:40:45 -0600 https://bioinformaticsonline.com/snippets/view/42563/install-asciigenome-using-conda (JitMetaENV) ➜ viruses conda install -c bioconda asciigenome Collecting package metadata (current_repodata.json): / done Solving environment: done ==> WARNING: A newer version of conda exists. <== current version: 4.9.0 latest version: 4.9.2 Please update conda by running $ conda update -n base -c defaults conda ## Package Plan ## environment location: /home/urbe/anaconda3/envs/JitMetaENV added / updated specs: - asciigenome The following NEW packages will be INSTALLED: asciigenome bioconda/noarch::asciigenome-1.16.0-0 Proceed ([y]/n)? Preparing transaction: done Verifying transaction: done Executing transaction: done]]> Jit https://bioinformaticsonline.com/snippets/view/42562/install-bwa-using-conda Wed, 06 Jan 2021 05:02:17 -0600 https://bioinformaticsonline.com/snippets/view/42562/install-bwa-using-conda (JitMetaENV) ➜ assembly conda install -c bioconda bwa Collecting package metadata (current_repodata.json): done Solving environment: done ==> WARNING: A newer version of conda exists. <== current version: 4.9.0 latest version: 4.9.2 Please update conda by running $ conda update -n base -c defaults conda ## Package Plan ## environment location: /home/urbe/anaconda3/envs/JitMetaENV added / updated specs: - bwa The following packages will be downloaded: package | build ---------------------------|----------------- bwa-0.7.17 | hed695b0_7 523 KB bioconda ------------------------------------------------------------ Total: 523 KB The following NEW packages will be INSTALLED: bwa bioconda/linux-64::bwa-0.7.17-hed695b0_7 Proceed ([y]/n)?]]> Jit https://bioinformaticsonline.com/snippets/view/42561/install-seqtk-using-conda Wed, 06 Jan 2021 04:51:34 -0600 https://bioinformaticsonline.com/snippets/view/42561/install-seqtk-using-conda (JitMetaENV) ➜ META_PE conda install -c bioconda seqtk Collecting package metadata (current_repodata.json): done Solving environment: done ==> WARNING: A newer version of conda exists. <== current version: 4.9.0 latest version: 4.9.2 Please update conda by running $ conda update -n base -c defaults conda ## Package Plan ## environment location: /home/urbe/anaconda3/envs/JitMetaENV added / updated specs: - seqtk The following NEW packages will be INSTALLED: seqtk bioconda/linux-64::seqtk-1.3-hed695b0_2 Proceed ([y]/n)?]]> Jit https://bioinformaticsonline.com/snippets/view/42558/genome-assembly-treasure-hunt Wed, 06 Jan 2021 02:40:02 -0600 https://bioinformaticsonline.com/snippets/view/42558/genome-assembly-treasure-hunt Use pen and paper the assemble it. If you are brave enough, you can try to assemble this set of reads: CAGATGTCCT GACCTTTTCT TAAGATCTTT TCTTTAGCCG TTTCTTCTTT GAGCTTTACT TTACTTCATT TCATTCACAT CACATGAGCT GTCCTGAACA GAGCTGATCA TCTTTCAGAT AGCCGGACCT TATGATCATT TCATTAGGCG AGGCGGAGCT HINT: There is NO sequencing errors HINT: Overlaps are at least of length 5]]> Jit https://bioinformaticsonline.com/snippets/view/42557/install-prokka-using-conda Wed, 06 Jan 2021 02:22:33 -0600 https://bioinformaticsonline.com/snippets/view/42557/install-prokka-using-conda (JitMetaENV) ➜ assembly conda install -c bioconda prokka Collecting package metadata (current_repodata.json): done Solving environment: failed with initial frozen solve. Retrying with flexible solve. Solving environment: failed with repodata from current_repodata.json, will retry with next repodata source. Collecting package metadata (repodata.json): done Solving environment: done ==> WARNING: A newer version of conda exists. <== current version: 4.9.0 latest version: 4.9.2 Please update conda by running $ conda update -n base -c defaults conda ## Package Plan ## environment location: /home/urbe/anaconda3/envs/JitMetaENV added / updated specs: - prokka The following packages will be downloaded: package | build ---------------------------|----------------- aragorn-1.2.38 | h516909a_3 139 KB bioconda barrnap-0.9 | 3 556 KB bioconda bedtools-2.29.2 | hc088bd4_0 13.8 MB bioconda cairo-1.16.0 | h9f066cc_1006 1.5 MB conda-forge fribidi-1.0.10 | h36c2ea0_0 112 KB conda-forge graphite2-1.3.13 | h58526e2_1001 102 KB conda-forge graphviz-2.42.3 | h0511662_0 6.9 MB conda-forge harfbuzz-2.7.2 | ha5b49bf_1 1.8 MB conda-forge hmmer-3.3.1 | he1b5a44_0 10.0 MB bioconda infernal-1.1.3 | h516909a_0 3.5 MB bioconda libdb-6.1.26 | 0 21.5 MB bioconda libgcc-7.2.0 | h69d50b8_2 304 KB conda-forge libglib-2.66.4 | h164308a_1 3.0 MB conda-forge libidn11-1.34 | h1cef754_0 227 KB conda-forge libtool-2.4.6 | h58526e2_1007 497 KB conda-forge libxslt-1.1.33 | hf705e74_1 540 KB conda-forge minced-0.4.2 | 0 46 KB bioconda paml-4.9 | h516909a_5 1.5 MB bioconda pango-1.42.4 | h69149e4_5 533 KB conda-forge parallel-20160622 | 1 1019 KB bioconda perl-aceperl-1.92 | pl526_2 149 KB bioconda perl-algorithm-diff-1.1903 | pl526_2 34 KB bioconda perl-algorithm-munkres-0.08| pl526_1 11 KB bioconda perl-apache-test-1.40 | pl526_1 115 KB bioconda perl-appconfig-1.71 | pl526_1 42 KB bioconda perl-array-compare-3.0.1 | pl526_1 12 KB bioconda perl-bio-asn1-entrezgene-1.73| pl526_1 23 KB bioconda perl-bio-coordinate-1.007001| pl526_1 34 KB bioconda perl-bio-featureio-1.6.905 | pl526_2 39 KB bioconda perl-bio-phylo-0.58 | pl526_2 301 KB bioconda perl-bio-samtools-1.43 | pl526h1341992_1 172 KB bioconda perl-bio-tools-phylo-paml-1.7.3| pl526_1 56 KB bioconda perl-bio-tools-run-alignment-clustalw-1.7.4| pl526_1 24 KB bioconda perl-bio-tools-run-alignment-tcoffee-1.7.4| pl526_2 23 KB bioconda perl-bioperl-1.7.2 | pl526_11 13 KB bioconda perl-bioperl-core-1.007002 | pl526_2 3.2 MB bioconda perl-bioperl-run-1.007002 | pl526_4 432 KB bioconda perl-cache-cache-1.08 | pl526_0 31 KB bioconda perl-capture-tiny-0.48 | pl526_0 17 KB bioconda perl-cgi-4.44 | pl526h14c3975_1 116 KB bioconda perl-class-data-inheritable-0.08| pl526_1 7 KB bioconda perl-class-inspector-1.34 | pl526_0 14 KB bioconda perl-class-load-0.25 | pl526_0 12 KB bioconda perl-class-load-xs-0.10 | pl526h6bb024c_2 13 KB bioconda perl-class-method-modifiers-2.12| pl526_0 13 KB bioconda perl-convert-binary-c-0.78 | pl526h6bb024c_3 252 KB bioconda perl-convert-binhex-1.125 | pl526_1 25 KB bioconda perl-crypt-rc4-2.02 | pl526_1 8 KB bioconda perl-data-optlist-0.110 | pl526_2 10 KB bioconda perl-data-stag-0.14 | pl526_1 78 KB bioconda perl-date-format-2.30 | pl526_2 29 KB bioconda perl-db-file-1.852 | pl526h14c3975_0 52 KB bioconda perl-dbd-sqlite-1.64 | pl526h516909a_0 2.3 MB bioconda perl-dbi-1.642 | pl526_0 549 KB bioconda perl-devel-globaldestruction-0.14| pl526_0 7 KB bioconda perl-devel-overloadinfo-0.005| pl526_0 8 KB bioconda perl-devel-stacktrace-2.04 | pl526_0 16 KB bioconda perl-digest-sha1-2.13 | pl526h6bb024c_1 20 KB bioconda perl-dist-checkconflicts-0.11| pl526_2 10 KB bioconda perl-email-date-format-1.005| pl526_2 8 KB bioconda perl-error-0.17027 | pl526_1 20 KB bioconda perl-eval-closure-0.14 | pl526h6bb024c_4 11 KB bioconda perl-exception-class-1.44 | pl526_0 19 KB bioconda perl-file-slurp-tiny-0.004 | pl526_1 8 KB bioconda perl-file-sort-1.01 | pl526_2 18 KB bioconda perl-file-which-1.23 | pl526_0 12 KB bioconda perl-font-afm-1.20 | pl526_2 14 KB bioconda perl-getopt-long-2.50 | pl526_1 27 KB bioconda perl-graph-0.9704 | pl526_1 73 KB bioconda perl-graphviz-2.24 | pl526h734ff71_0 36 KB bioconda perl-html-element-extended-1.18| pl526_1 24 KB bioconda perl-html-entities-numbered-0.04| pl526_1 11 KB bioconda perl-html-formatter-2.16 | pl526_0 30 KB bioconda perl-html-tableextract-2.13| pl526_2 23 KB bioconda perl-html-tidy-1.60 | pl526_0 20 KB bioconda perl-html-treebuilder-xpath-0.14| pl526_1 12 KB bioconda perl-image-info-1.38 | pl526_1 41 KB bioconda perl-image-size-3.300 | pl526_2 26 KB bioconda perl-io-sessiondata-1.03 | pl526_1 8 KB bioconda perl-io-stringy-2.111 | pl526_1 35 KB bioconda perl-io-tty-1.12 | pl526_1 30 KB bioconda perl-ipc-run-20180523.0 | pl526_0 74 KB bioconda perl-ipc-sharelite-0.17 | pl526h6bb024c_1 24 KB bioconda perl-jcode-2.07 | pl526_2 24 KB bioconda perl-lib-0.63 | pl526_1 6 KB bioconda perl-libxml-perl-0.08 | pl526_2 38 KB bioconda perl-lwp-simple-6.15 | pl526h470a237_4 348 KB bioconda perl-mailtools-2.21 | pl526_0 48 KB bioconda perl-math-cdf-0.1 | pl526h14c3975_5 69 KB bioconda perl-math-derivative-1.01 | pl526_0 9 KB bioconda perl-math-random-0.72 | pl526h14c3975_2 55 KB bioconda perl-math-spline-0.02 | pl526_2 8 KB bioconda perl-mime-lite-3.030 | pl526_1 51 KB bioconda perl-mime-tools-5.508 | pl526_1 113 KB bioconda perl-mime-types-2.17 | pl526_0 56 KB bioconda perl-mldbm-2.05 | pl526_1 15 KB bioconda perl-module-runtime-conflicts-0.003| pl526_0 7 KB bioconda perl-moo-2.003004 | pl526_0 38 KB bioconda perl-moose-2.2011 | pl526hf484d3e_1 444 KB bioconda perl-mro-compat-0.13 | pl526_0 10 KB bioconda perl-ole-storage_lite-0.19 | pl526_3 18 KB bioconda perl-package-deprecationmanager-0.17| pl526_0 10 KB bioconda perl-package-stash-0.38 | pl526hf484d3e_1 66 KB bioconda perl-package-stash-xs-0.28 | pl526hf484d3e_1 21 KB bioconda perl-params-util-1.07 | pl526h6bb024c_4 14 KB bioconda perl-parse-recdescent-1.967015| pl526_0 71 KB bioconda perl-pdf-api2-2.035 | pl526_0 2.3 MB bioconda perl-pod-escapes-1.07 | pl526_1 10 KB bioconda perl-pod-usage-1.69 | pl526_1 13 KB bioconda perl-postscript-0.06 | pl526_2 22 KB bioconda perl-role-tiny-2.000008 | pl526_0 15 KB bioconda perl-set-scalar-1.29 | pl526_2 19 KB bioconda perl-soap-lite-1.19 | pl526_1 117 KB bioconda perl-sort-naturally-1.03 | pl526_2 14 KB bioconda perl-spreadsheet-parseexcel-0.65| pl526_2 63 KB bioconda perl-spreadsheet-writeexcel-2.40| pl526_2 259 KB bioconda perl-statistics-descriptive-3.0702| pl526_0 32 KB bioconda perl-sub-exporter-0.987 | pl526_2 30 KB bioconda perl-sub-exporter-progressive-0.001013| pl526_0 8 KB bioconda perl-sub-identify-0.14 | pl526h14c3975_0 12 KB bioconda perl-sub-install-0.928 | pl526_2 10 KB bioconda perl-sub-name-0.21 | pl526_1 13 KB bioconda perl-sub-quote-2.006003 | pl526_1 18 KB bioconda perl-sub-uplevel-0.2800 | pl526h14c3975_2 13 KB bioconda perl-svg-graph-0.02 | pl526_3 26 KB bioconda perl-task-weaken-1.06 | pl526_0 8 KB bioconda perl-template-toolkit-2.26 | pl526_1 319 KB bioconda perl-test-1.26 | pl526_1 14 KB bioconda perl-test-deep-1.128 | pl526_1 36 KB bioconda perl-test-differences-0.67 | pl526_0 15 KB bioconda perl-test-exception-0.43 | pl526_2 12 KB bioconda perl-test-harness-3.42 | pl526_0 82 KB bioconda perl-test-leaktrace-0.16 | pl526h14c3975_2 23 KB bioconda perl-test-most-0.35 | pl526_0 18 KB bioconda perl-test-warn-0.36 | pl526_1 13 KB bioconda perl-text-diff-1.45 | pl526_0 20 KB bioconda perl-threaded-5.26.0 | 0 4 KB bioconda perl-tie-ixhash-1.23 | pl526_2 11 KB bioconda perl-timedate-2.30 | pl526_1 29 KB bioconda perl-tree-dag_node-1.31 | pl526_0 40 KB bioconda perl-type-tiny-1.004004 | pl526_0 119 KB bioconda perl-unicode-map-0.112 | pl526h6bb024c_3 254 KB bioconda perl-xml-dom-1.46 | pl526_0 56 KB bioconda perl-xml-dom-xpath-0.14 | pl526_1 9 KB bioconda perl-xml-filter-buffertext-1.01| pl526_2 7 KB bioconda perl-xml-libxslt-1.94 | pl526_1 40 KB bioconda perl-xml-regexp-0.04 | pl526_2 8 KB bioconda perl-xml-sax-writer-0.57 | pl526_0 16 KB bioconda perl-xml-twig-3.52 | pl526_2 144 KB bioconda perl-xml-writer-0.625 | pl526_2 18 KB bioconda perl-xml-xpath-1.44 | pl526_0 42 KB bioconda perl-xml-xpathengine-0.14 | pl526_2 26 KB bioconda perl-yaml-1.29 | pl526_0 41 KB bioconda pixman-0.40.0 | h36c2ea0_0 627 KB conda-forge prodigal-2.6.3 | h516909a_2 777 KB bioconda prokka-1.13 | 3 188.4 MB bioconda pthread-stubs-0.4 | h36c2ea0_1001 5 KB conda-forge t_coffee-11.0.8 | py36hea885bf_8 33.2 MB bioconda tbl2asn-25.7 | 0 4.3 MB bioconda tidyp-1.04 | h516909a_2 286 KB bioconda xorg-xproto-7.0.31 | h7f98852_1007 73 KB conda-forge ------------------------------------------------------------ Total: 309.5 MB The following NEW packages will be INSTALLED: aragorn bioconda/linux-64::aragorn-1.2.38-h516909a_3 barrnap bioconda/noarch::barrnap-0.9-3 bedtools bioconda/linux-64::bedtools-2.29.2-hc088bd4_0 cairo conda-forge/linux-64::cairo-1.16.0-h9f066cc_1006 clustalw bioconda/linux-64::clustalw-2.1-hc9558a2_5 fribidi conda-forge/linux-64::fribidi-1.0.10-h36c2ea0_0 graphite2 conda-forge/linux-64::graphite2-1.3.13-h58526e2_1001 graphviz conda-forge/linux-64::graphviz-2.42.3-h0511662_0 harfbuzz conda-forge/linux-64::harfbuzz-2.7.2-ha5b49bf_1 hmmer bioconda/linux-64::hmmer-3.3.1-he1b5a44_0 infernal bioconda/linux-64::infernal-1.1.3-h516909a_0 libdb bioconda/linux-64::libdb-6.1.26-0 libgcc conda-forge/linux-64::libgcc-7.2.0-h69d50b8_2 libglib conda-forge/linux-64::libglib-2.66.4-h164308a_1 libidn11 conda-forge/linux-64::libidn11-1.34-h1cef754_0 libtool conda-forge/linux-64::libtool-2.4.6-h58526e2_1007 libxcb conda-forge/linux-64::libxcb-1.13-h14c3975_1002 libxslt conda-forge/linux-64::libxslt-1.1.33-hf705e74_1 minced bioconda/noarch::minced-0.4.2-0 paml bioconda/linux-64::paml-4.9-h516909a_5 pango conda-forge/linux-64::pango-1.42.4-h69149e4_5 parallel bioconda/linux-64::parallel-20160622-1 perl-aceperl bioconda/linux-64::perl-aceperl-1.92-pl526_2 perl-algorithm-di~ bioconda/linux-64::perl-algorithm-diff-1.1903-pl526_2 perl-algorithm-mu~ bioconda/linux-64::perl-algorithm-munkres-0.08-pl526_1 perl-apache-test bioconda/linux-64::perl-apache-test-1.40-pl526_1 perl-appconfig bioconda/linux-64::perl-appconfig-1.71-pl526_1 perl-array-compare bioconda/linux-64::perl-array-compare-3.0.1-pl526_1 perl-bio-asn1-ent~ bioconda/noarch::perl-bio-asn1-entrezgene-1.73-pl526_1 perl-bio-coordina~ bioconda/noarch::perl-bio-coordinate-1.007001-pl526_1 perl-bio-featureio bioconda/noarch::perl-bio-featureio-1.6.905-pl526_2 perl-bio-phylo bioconda/noarch::perl-bio-phylo-0.58-pl526_2 perl-bio-samtools bioconda/linux-64::perl-bio-samtools-1.43-pl526h1341992_1 perl-bio-tools-ph~ bioconda/noarch::perl-bio-tools-phylo-paml-1.7.3-pl526_1 perl-bio-tools-ru~ bioconda/noarch::perl-bio-tools-run-alignment-clustalw-1.7.4-pl526_1 perl-bio-tools-ru~ bioconda/noarch::perl-bio-tools-run-alignment-tcoffee-1.7.4-pl526_2 perl-bioperl bioconda/noarch::perl-bioperl-1.7.2-pl526_11 perl-bioperl-core bioconda/noarch::perl-bioperl-core-1.007002-pl526_2 perl-bioperl-run bioconda/noarch::perl-bioperl-run-1.007002-pl526_4 perl-cache-cache bioconda/linux-64::perl-cache-cache-1.08-pl526_0 perl-capture-tiny bioconda/linux-64::perl-capture-tiny-0.48-pl526_0 perl-cgi bioconda/linux-64::perl-cgi-4.44-pl526h14c3975_1 perl-class-data-i~ bioconda/linux-64::perl-class-data-inheritable-0.08-pl526_1 perl-class-inspec~ bioconda/linux-64::perl-class-inspector-1.34-pl526_0 perl-class-load bioconda/linux-64::perl-class-load-0.25-pl526_0 perl-class-load-xs bioconda/linux-64::perl-class-load-xs-0.10-pl526h6bb024c_2 perl-class-method~ bioconda/linux-64::perl-class-method-modifiers-2.12-pl526_0 perl-convert-bina~ bioconda/linux-64::perl-convert-binary-c-0.78-pl526h6bb024c_3 perl-convert-binh~ bioconda/linux-64::perl-convert-binhex-1.125-pl526_1 perl-crypt-rc4 bioconda/linux-64::perl-crypt-rc4-2.02-pl526_1 perl-data-optlist bioconda/linux-64::perl-data-optlist-0.110-pl526_2 perl-data-stag bioconda/linux-64::perl-data-stag-0.14-pl526_1 perl-date-format bioconda/linux-64::perl-date-format-2.30-pl526_2 perl-db-file bioconda/linux-64::perl-db-file-1.852-pl526h14c3975_0 perl-dbd-sqlite bioconda/linux-64::perl-dbd-sqlite-1.64-pl526h516909a_0 perl-dbi bioconda/linux-64::perl-dbi-1.642-pl526_0 perl-devel-global~ bioconda/linux-64::perl-devel-globaldestruction-0.14-pl526_0 perl-devel-overlo~ bioconda/linux-64::perl-devel-overloadinfo-0.005-pl526_0 perl-devel-stackt~ bioconda/noarch::perl-devel-stacktrace-2.04-pl526_0 perl-digest-sha1 bioconda/linux-64::perl-digest-sha1-2.13-pl526h6bb024c_1 perl-dist-checkco~ bioconda/linux-64::perl-dist-checkconflicts-0.11-pl526_2 perl-email-date-f~ bioconda/linux-64::perl-email-date-format-1.005-pl526_2 perl-error bioconda/linux-64::perl-error-0.17027-pl526_1 perl-eval-closure bioconda/linux-64::perl-eval-closure-0.14-pl526h6bb024c_4 perl-exception-cl~ bioconda/linux-64::perl-exception-class-1.44-pl526_0 perl-file-slurp-t~ bioconda/linux-64::perl-file-slurp-tiny-0.004-pl526_1 perl-file-sort bioconda/linux-64::perl-file-sort-1.01-pl526_2 perl-file-which bioconda/linux-64::perl-file-which-1.23-pl526_0 perl-font-afm bioconda/linux-64::perl-font-afm-1.20-pl526_2 perl-getopt-long bioconda/linux-64::perl-getopt-long-2.50-pl526_1 perl-graph bioconda/linux-64::perl-graph-0.9704-pl526_1 perl-graphviz bioconda/linux-64::perl-graphviz-2.24-pl526h734ff71_0 perl-html-element~ bioconda/linux-64::perl-html-element-extended-1.18-pl526_1 perl-html-entitie~ bioconda/linux-64::perl-html-entities-numbered-0.04-pl526_1 perl-html-formatt~ bioconda/linux-64::perl-html-formatter-2.16-pl526_0 perl-html-tableex~ bioconda/linux-64::perl-html-tableextract-2.13-pl526_2 perl-html-tidy bioconda/linux-64::perl-html-tidy-1.60-pl526_0 perl-html-treebui~ bioconda/linux-64::perl-html-treebuilder-xpath-0.14-pl526_1 perl-image-info bioconda/linux-64::perl-image-info-1.38-pl526_1 perl-image-size bioconda/linux-64::perl-image-size-3.300-pl526_2 perl-io-sessionda~ bioconda/linux-64::perl-io-sessiondata-1.03-pl526_1 perl-io-stringy bioconda/linux-64::perl-io-stringy-2.111-pl526_1 perl-io-tty bioconda/linux-64::perl-io-tty-1.12-pl526_1 perl-ipc-run bioconda/linux-64::perl-ipc-run-20180523.0-pl526_0 perl-ipc-sharelite bioconda/linux-64::perl-ipc-sharelite-0.17-pl526h6bb024c_1 perl-jcode bioconda/linux-64::perl-jcode-2.07-pl526_2 perl-lib bioconda/linux-64::perl-lib-0.63-pl526_1 perl-libxml-perl bioconda/linux-64::perl-libxml-perl-0.08-pl526_2 perl-lwp-simple bioconda/linux-64::perl-lwp-simple-6.15-pl526h470a237_4 perl-mailtools bioconda/noarch::perl-mailtools-2.21-pl526_0 perl-math-cdf bioconda/linux-64::perl-math-cdf-0.1-pl526h14c3975_5 perl-math-derivat~ bioconda/linux-64::perl-math-derivative-1.01-pl526_0 perl-math-random bioconda/linux-64::perl-math-random-0.72-pl526h14c3975_2 perl-math-spline bioconda/linux-64::perl-math-spline-0.02-pl526_2 perl-mime-lite bioconda/linux-64::perl-mime-lite-3.030-pl526_1 perl-mime-tools bioconda/linux-64::perl-mime-tools-5.508-pl526_1 perl-mime-types bioconda/linux-64::perl-mime-types-2.17-pl526_0 perl-mldbm bioconda/linux-64::perl-mldbm-2.05-pl526_1 perl-module-runti~ bioconda/linux-64::perl-module-runtime-conflicts-0.003-pl526_0 perl-moo bioconda/linux-64::perl-moo-2.003004-pl526_0 perl-moose bioconda/linux-64::perl-moose-2.2011-pl526hf484d3e_1 perl-mro-compat bioconda/linux-64::perl-mro-compat-0.13-pl526_0 perl-ole-storage_~ bioconda/linux-64::perl-ole-storage_lite-0.19-pl526_3 perl-package-depr~ bioconda/linux-64::perl-package-deprecationmanager-0.17-pl526_0 perl-package-stash bioconda/linux-64::perl-package-stash-0.38-pl526hf484d3e_1 perl-package-stas~ bioconda/linux-64::perl-package-stash-xs-0.28-pl526hf484d3e_1 perl-params-util bioconda/linux-64::perl-params-util-1.07-pl526h6bb024c_4 perl-parse-recdes~ bioconda/linux-64::perl-parse-recdescent-1.967015-pl526_0 perl-pdf-api2 bioconda/noarch::perl-pdf-api2-2.035-pl526_0 perl-pod-escapes bioconda/linux-64::perl-pod-escapes-1.07-pl526_1 perl-pod-usage bioconda/linux-64::perl-pod-usage-1.69-pl526_1 perl-postscript bioconda/linux-64::perl-postscript-0.06-pl526_2 perl-role-tiny bioconda/noarch::perl-role-tiny-2.000008-pl526_0 perl-set-scalar bioconda/linux-64::perl-set-scalar-1.29-pl526_2 perl-soap-lite bioconda/linux-64::perl-soap-lite-1.19-pl526_1 perl-sort-natural~ bioconda/linux-64::perl-sort-naturally-1.03-pl526_2 perl-spreadsheet-~ bioconda/linux-64::perl-spreadsheet-parseexcel-0.65-pl526_2 perl-spreadsheet-~ bioconda/linux-64::perl-spreadsheet-writeexcel-2.40-pl526_2 perl-statistics-d~ bioconda/linux-64::perl-statistics-descriptive-3.0702-pl526_0 perl-sub-exporter bioconda/linux-64::perl-sub-exporter-0.987-pl526_2 perl-sub-exporter~ bioconda/linux-64::perl-sub-exporter-progressive-0.001013-pl526_0 perl-sub-identify bioconda/linux-64::perl-sub-identify-0.14-pl526h14c3975_0 perl-sub-install bioconda/linux-64::perl-sub-install-0.928-pl526_2 perl-sub-name bioconda/linux-64::perl-sub-name-0.21-pl526_1 perl-sub-quote bioconda/linux-64::perl-sub-quote-2.006003-pl526_1 perl-sub-uplevel bioconda/linux-64::perl-sub-uplevel-0.2800-pl526h14c3975_2 perl-svg-graph bioconda/linux-64::perl-svg-graph-0.02-pl526_3 perl-task-weaken bioconda/linux-64::perl-task-weaken-1.06-pl526_0 perl-template-too~ bioconda/linux-64::perl-template-toolkit-2.26-pl526_1 perl-test bioconda/linux-64::perl-test-1.26-pl526_1 perl-test-deep bioconda/linux-64::perl-test-deep-1.128-pl526_1 perl-test-differe~ bioconda/noarch::perl-test-differences-0.67-pl526_0 perl-test-excepti~ bioconda/linux-64::perl-test-exception-0.43-pl526_2 perl-test-harness bioconda/linux-64::perl-test-harness-3.42-pl526_0 perl-test-leaktra~ bioconda/linux-64::perl-test-leaktrace-0.16-pl526h14c3975_2 perl-test-most bioconda/linux-64::perl-test-most-0.35-pl526_0 perl-test-warn bioconda/linux-64::perl-test-warn-0.36-pl526_1 perl-text-diff bioconda/linux-64::perl-text-diff-1.45-pl526_0 perl-threaded bioconda/linux-64::perl-threaded-5.26.0-0 perl-tie-ixhash bioconda/linux-64::perl-tie-ixhash-1.23-pl526_2 perl-timedate bioconda/linux-64::perl-timedate-2.30-pl526_1 perl-tree-dag_node bioconda/linux-64::perl-tree-dag_node-1.31-pl526_0 perl-type-tiny bioconda/linux-64::perl-type-tiny-1.004004-pl526_0 perl-unicode-map bioconda/linux-64::perl-unicode-map-0.112-pl526h6bb024c_3 perl-xml-dom bioconda/linux-64::perl-xml-dom-1.46-pl526_0 perl-xml-dom-xpath bioconda/linux-64::perl-xml-dom-xpath-0.14-pl526_1 perl-xml-filter-b~ bioconda/linux-64::perl-xml-filter-buffertext-1.01-pl526_2 perl-xml-libxslt bioconda/linux-64::perl-xml-libxslt-1.94-pl526_1 perl-xml-regexp bioconda/linux-64::perl-xml-regexp-0.04-pl526_2 perl-xml-sax-writ~ bioconda/linux-64::perl-xml-sax-writer-0.57-pl526_0 perl-xml-twig bioconda/linux-64::perl-xml-twig-3.52-pl526_2 perl-xml-writer bioconda/linux-64::perl-xml-writer-0.625-pl526_2 perl-xml-xpath bioconda/linux-64::perl-xml-xpath-1.44-pl526_0 perl-xml-xpatheng~ bioconda/linux-64::perl-xml-xpathengine-0.14-pl526_2 perl-yaml bioconda/noarch::perl-yaml-1.29-pl526_0 pixman conda-forge/linux-64::pixman-0.40.0-h36c2ea0_0 prodigal bioconda/linux-64::prodigal-2.6.3-h516909a_2 prokka bioconda/linux-64::prokka-1.13-3 pthread-stubs conda-forge/linux-64::pthread-stubs-0.4-h36c2ea0_1001 t_coffee bioconda/linux-64::t_coffee-11.0.8-py36hea885bf_8 tbl2asn bioconda/linux-64::tbl2asn-25.7-0 tidyp bioconda/linux-64::tidyp-1.04-h516909a_2 xorg-kbproto conda-forge/linux-64::xorg-kbproto-1.0.7-h14c3975_1002 xorg-libice conda-forge/linux-64::xorg-libice-1.0.10-h516909a_0 xorg-libsm conda-forge/linux-64::xorg-libsm-1.2.3-h84519dc_1000 xorg-libx11 conda-forge/linux-64::xorg-libx11-1.6.12-h516909a_0 xorg-libxau conda-forge/linux-64::xorg-libxau-1.0.9-h14c3975_0 xorg-libxdmcp conda-forge/linux-64::xorg-libxdmcp-1.1.3-h516909a_0 xorg-libxext conda-forge/linux-64::xorg-libxext-1.3.4-h516909a_0 xorg-libxpm conda-forge/linux-64::xorg-libxpm-3.5.13-h516909a_0 xorg-libxrender conda-forge/linux-64::xorg-libxrender-0.9.10-h516909a_1002 xorg-libxt conda-forge/linux-64::xorg-libxt-1.1.5-h516909a_1003 xorg-renderproto conda-forge/linux-64::xorg-renderproto-0.11.1-h14c3975_1002 xorg-xextproto conda-forge/linux-64::xorg-xextproto-7.3.0-h14c3975_1002 xorg-xproto conda-forge/linux-64::xorg-xproto-7.0.31-h7f98852_1007 Proceed ([y]/n)?]]> Jit https://bioinformaticsonline.com/snippets/view/42556/install-quast-using-conda Wed, 06 Jan 2021 02:11:25 -0600 https://bioinformaticsonline.com/snippets/view/42556/install-quast-using-conda (JitMetaENV) ➜ ~ conda install -c bioconda quast Collecting package metadata (current_repodata.json): done Solving environment: done ==> WARNING: A newer version of conda exists. <== current version: 4.9.0 latest version: 4.9.2 Please update conda by running $ conda update -n base -c defaults conda ## Package Plan ## environment location: /home/urbe/anaconda3/envs/JitMetaENV added / updated specs: - quast The following packages will be downloaded: package | build ---------------------------|----------------- circos-0.69.8 | 0 26.3 MB bioconda cycler-0.10.0 | py_2 9 KB conda-forge fontconfig-2.13.1 | h7e3eb15_1002 324 KB conda-forge giflib-5.2.1 | h36c2ea0_2 77 KB conda-forge glimmerhmm-3.0.4 | pl526hf484d3e_3 40.6 MB bioconda joblib-1.0.0 | pyhd8ed1ab_0 206 KB conda-forge jpeg-9d | h36c2ea0_0 264 KB conda-forge k8-0.2.5 | he513fc3_0 1.7 MB bioconda kiwisolver-1.3.1 | py36h51d7077_0 86 KB conda-forge lcms2-2.11 | hcbb858e_1 434 KB conda-forge libblas-3.9.0 | 6_openblas 11 KB conda-forge libcblas-3.9.0 | 6_openblas 11 KB conda-forge libgd-2.2.5 | h6e6070c_1008 297 KB conda-forge liblapack-3.9.0 | 6_openblas 11 KB conda-forge libopenblas-0.3.12 |pthreads_h4812303_1 8.9 MB conda-forge libtiff-4.2.0 | hdc55705_0 633 KB conda-forge libwebp-1.1.0 | h76fa15c_4 84 KB conda-forge libwebp-base-1.1.0 | h36c2ea0_3 864 KB conda-forge lz4-c-1.9.3 | h9c3ff4c_0 179 KB conda-forge matplotlib-base-3.3.3 | py36he12231b_0 6.8 MB conda-forge minimap2-2.17 | hed695b0_3 393 KB bioconda numpy-1.19.5 | py36h2aa4a07_0 5.3 MB conda-forge olefile-0.46 | pyh9f0ad1d_1 32 KB conda-forge perl-autoloader-5.74 | pl526_2 5 KB bioconda perl-clone-0.42 | pl526h516909a_0 13 KB bioconda perl-config-general-2.63 | pl526_0 41 KB bioconda perl-digest-perl-md5-1.9 | pl526_1 11 KB bioconda perl-dynaloader-1.25 | pl526_1 3 KB bioconda perl-font-ttf-1.06 | pl526_0 200 KB bioconda perl-gd-2.71 | pl526he860b03_0 114 KB bioconda perl-io-string-1.08 | pl526_3 10 KB bioconda perl-math-bezier-0.01 | pl526_1 8 KB bioconda perl-math-round-0.07 | pl526_1 9 KB bioconda perl-math-vecstat-0.08 | pl526_1 9 KB bioconda perl-module-implementation-0.09| pl526_2 9 KB bioconda perl-module-runtime-0.016 | pl526_1 15 KB bioconda perl-number-format-1.75 | pl526_3 20 KB bioconda perl-params-validate-1.29 | pl526h14c3975_1 25 KB bioconda perl-readonly-2.05 | pl526_0 17 KB bioconda perl-regexp-common-2017060201| pl526_0 93 KB bioconda perl-set-intspan-1.19 | pl526_1 22 KB bioconda perl-statistics-basic-1.6611| pl526_2 32 KB bioconda perl-svg-2.84 | pl526_0 37 KB bioconda perl-text-format-0.59 | pl526_2 16 KB bioconda perl-time-hires-1.9760 | pl526h14c3975_1 25 KB bioconda pillow-8.1.0 | py36h4f9996e_0 675 KB conda-forge pyparsing-2.4.7 | pyh9f0ad1d_0 60 KB conda-forge quast-5.0.2 |py36pl526h955c1b8_2 14.3 MB bioconda simplejson-3.8.1 | py36_0 130 KB bioconda tornado-6.1 | py36h1d69622_0 644 KB conda-forge zstd-1.4.8 | ha95c52a_1 702 KB conda-forge ------------------------------------------------------------ Total: 110.5 MB The following NEW packages will be INSTALLED: circos bioconda/noarch::circos-0.69.8-0 cycler conda-forge/noarch::cycler-0.10.0-py_2 giflib conda-forge/linux-64::giflib-5.2.1-h36c2ea0_2 glimmerhmm bioconda/linux-64::glimmerhmm-3.0.4-pl526hf484d3e_3 joblib conda-forge/noarch::joblib-1.0.0-pyhd8ed1ab_0 jpeg conda-forge/linux-64::jpeg-9d-h36c2ea0_0 k8 bioconda/linux-64::k8-0.2.5-he513fc3_0 kiwisolver conda-forge/linux-64::kiwisolver-1.3.1-py36h51d7077_0 lcms2 conda-forge/linux-64::lcms2-2.11-hcbb858e_1 libblas conda-forge/linux-64::libblas-3.9.0-6_openblas libcblas conda-forge/linux-64::libcblas-3.9.0-6_openblas libgd conda-forge/linux-64::libgd-2.2.5-h6e6070c_1008 liblapack conda-forge/linux-64::liblapack-3.9.0-6_openblas libopenblas conda-forge/linux-64::libopenblas-0.3.12-pthreads_h4812303_1 libtiff conda-forge/linux-64::libtiff-4.2.0-hdc55705_0 libwebp conda-forge/linux-64::libwebp-1.1.0-h76fa15c_4 libwebp-base conda-forge/linux-64::libwebp-base-1.1.0-h36c2ea0_3 lz4-c conda-forge/linux-64::lz4-c-1.9.3-h9c3ff4c_0 matplotlib-base conda-forge/linux-64::matplotlib-base-3.3.3-py36he12231b_0 minimap2 bioconda/linux-64::minimap2-2.17-hed695b0_3 numpy conda-forge/linux-64::numpy-1.19.5-py36h2aa4a07_0 olefile conda-forge/noarch::olefile-0.46-pyh9f0ad1d_1 perl-autoloader bioconda/linux-64::perl-autoloader-5.74-pl526_2 perl-clone bioconda/linux-64::perl-clone-0.42-pl526h516909a_0 perl-config-gener~ bioconda/linux-64::perl-config-general-2.63-pl526_0 perl-digest-perl-~ bioconda/linux-64::perl-digest-perl-md5-1.9-pl526_1 perl-dynaloader bioconda/linux-64::perl-dynaloader-1.25-pl526_1 perl-font-ttf bioconda/linux-64::perl-font-ttf-1.06-pl526_0 perl-gd bioconda/linux-64::perl-gd-2.71-pl526he860b03_0 perl-io-string bioconda/linux-64::perl-io-string-1.08-pl526_3 perl-math-bezier bioconda/linux-64::perl-math-bezier-0.01-pl526_1 perl-math-round bioconda/linux-64::perl-math-round-0.07-pl526_1 perl-math-vecstat bioconda/linux-64::perl-math-vecstat-0.08-pl526_1 perl-module-imple~ bioconda/linux-64::perl-module-implementation-0.09-pl526_2 perl-module-runti~ bioconda/linux-64::perl-module-runtime-0.016-pl526_1 perl-number-format bioconda/linux-64::perl-number-format-1.75-pl526_3 perl-params-valid~ bioconda/linux-64::perl-params-validate-1.29-pl526h14c3975_1 perl-readonly bioconda/linux-64::perl-readonly-2.05-pl526_0 perl-regexp-common bioconda/linux-64::perl-regexp-common-2017060201-pl526_0 perl-set-intspan bioconda/linux-64::perl-set-intspan-1.19-pl526_1 perl-statistics-b~ bioconda/linux-64::perl-statistics-basic-1.6611-pl526_2 perl-svg bioconda/linux-64::perl-svg-2.84-pl526_0 perl-text-format bioconda/linux-64::perl-text-format-0.59-pl526_2 perl-time-hires bioconda/linux-64::perl-time-hires-1.9760-pl526h14c3975_1 pillow conda-forge/linux-64::pillow-8.1.0-py36h4f9996e_0 pyparsing conda-forge/noarch::pyparsing-2.4.7-pyh9f0ad1d_0 python-dateutil conda-forge/noarch::python-dateutil-2.8.1-py_0 quast bioconda/linux-64::quast-5.0.2-py36pl526h955c1b8_2 simplejson bioconda/linux-64::simplejson-3.8.1-py36_0 six conda-forge/noarch::six-1.15.0-pyh9f0ad1d_0 tornado conda-forge/linux-64::tornado-6.1-py36h1d69622_0 zstd conda-forge/linux-64::zstd-1.4.8-ha95c52a_1 The following packages will be DOWNGRADED: fontconfig 2.13.1-h736d332_1003 --> 2.13.1-h7e3eb15_1002 icu 68.1-h58526e2_0 --> 67.1-he1b5a44_0 libxml2 2.9.10-h72842e0_3 --> 2.9.10-h68273f3_2 Proceed ([y]/n)?]]> Jit https://bioinformaticsonline.com/snippets/view/42555/python-script-to-check-sequence-length-in-multifasta-file Wed, 06 Jan 2021 01:38:26 -0600 https://bioinformaticsonline.com/snippets/view/42555/python-script-to-check-sequence-length-in-multifasta-file #!/usr/bin/python from Bio import SeqIO import sys cmdargs = str(sys.argv) for seq_record in SeqIO.parse(str(sys.argv[1]), "fasta"): output_line = '%s\t%i' % \ (seq_record.id, len(seq_record)) print(output_line)]]> Jit https://bioinformaticsonline.com/snippets/view/42551/install-kraken2-using-conda Tue, 05 Jan 2021 21:56:04 -0600 https://bioinformaticsonline.com/snippets/view/42551/install-kraken2-using-conda (JitMetaENV) ➜ day2 conda install -c bioconda kraken2 Collecting package metadata (current_repodata.json): done Solving environment: failed with initial frozen solve. Retrying with flexible solve. Solving environment: failed with repodata from current_repodata.json, will retry with next repodata source. Collecting package metadata (repodata.json): done Solving environment: done ==> WARNING: A newer version of conda exists. <== current version: 4.9.0 latest version: 4.9.2 Please update conda by running $ conda update -n base -c defaults conda ## Package Plan ## environment location: /home/urbe/anaconda3/envs/JitMetaENV added / updated specs: - kraken2 The following packages will be downloaded: package | build ---------------------------|----------------- blast-2.10.1 | pl526he19e7b1_3 20.6 MB bioconda entrez-direct-13.9 | pl526h375a9b1_0 5.5 MB bioconda kraken2-2.1.1 | pl526hc9558a2_0 203 KB bioconda perl-archive-tar-2.32 | pl526_0 31 KB bioconda perl-base-2.23 | pl526_1 10 KB bioconda perl-common-sense-3.74 | pl526_2 11 KB bioconda perl-compress-raw-bzip2-2.087| pl526he1b5a44_0 44 KB bioconda perl-compress-raw-zlib-2.087| pl526hc9558a2_0 72 KB bioconda perl-digest-hmac-1.03 | pl526_3 9 KB bioconda perl-digest-md5-2.55 | pl526_0 18 KB bioconda perl-encode-locale-1.05 | pl526_6 11 KB bioconda perl-exporter-tiny-1.002001| pl526_0 23 KB bioconda perl-file-listing-6.04 | pl526_1 9 KB bioconda perl-html-parser-3.72 | pl526h6bb024c_5 66 KB bioconda perl-html-tagset-3.20 | pl526_3 12 KB bioconda perl-html-tree-5.07 | pl526_1 129 KB bioconda perl-http-cookies-6.04 | pl526_0 19 KB bioconda perl-http-daemon-6.01 | pl526_1 14 KB bioconda perl-http-date-6.02 | pl526_3 10 KB bioconda perl-http-message-6.18 | pl526_0 51 KB bioconda perl-http-negotiate-6.01 | pl526_3 13 KB bioconda perl-io-compress-2.087 | pl526he1b5a44_0 81 KB bioconda perl-io-html-1.001 | pl526_2 13 KB bioconda perl-io-socket-ssl-2.066 | pl526_0 151 KB bioconda perl-io-zlib-1.10 | pl526_2 9 KB bioconda perl-json-4.02 | pl526_0 52 KB bioconda perl-json-xs-2.34 | pl526h6bb024c_3 63 KB bioconda perl-libwww-perl-6.39 | pl526_0 94 KB bioconda perl-list-moreutils-0.428 | pl526_1 28 KB bioconda perl-list-moreutils-xs-0.428| pl526_0 43 KB bioconda perl-lwp-mediatypes-6.04 | pl526_0 22 KB bioconda perl-lwp-protocol-https-6.07| pl526_4 9 KB bioconda perl-mozilla-ca-20180117 | pl526_1 140 KB bioconda perl-net-http-6.19 | pl526_0 19 KB bioconda perl-net-ssleay-1.88 | pl526h90d6eec_0 289 KB bioconda perl-ntlm-1.09 | pl526_4 15 KB bioconda perl-pathtools-3.75 | pl526h14c3975_1 41 KB bioconda perl-scalar-list-utils-1.52| pl526h516909a_0 38 KB bioconda perl-socket-2.027 | pl526_1 31 KB bioconda perl-storable-3.15 | pl526h14c3975_0 63 KB bioconda perl-test-requiresinternet-0.05| pl526_0 7 KB bioconda perl-time-local-1.28 | pl526_1 10 KB bioconda perl-try-tiny-0.30 | pl526_1 17 KB bioconda perl-types-serialiser-1.0 | pl526_2 10 KB bioconda perl-www-robotrules-6.02 | pl526_3 12 KB bioconda perl-xml-parser-2.44 | pl526h4e0c4b3_7 165 KB bioconda perl-xml-sax-expat-0.51 | pl526_3 10 KB bioconda perl-xml-simple-2.25 | pl526_1 48 KB bioconda popt-1.16 | 1 171 KB bioconda rsync-3.1.3 | h1245774_1003 286 KB conda-forge tar-1.32 | hd4ba37b_0 891 KB conda-forge ------------------------------------------------------------ Total: 29.6 MB The following NEW packages will be INSTALLED: blast bioconda/linux-64::blast-2.10.1-pl526he19e7b1_3 entrez-direct bioconda/linux-64::entrez-direct-13.9-pl526h375a9b1_0 expat conda-forge/linux-64::expat-2.2.9-he1b5a44_2 kraken2 bioconda/linux-64::kraken2-2.1.1-pl526hc9558a2_0 pcre conda-forge/linux-64::pcre-8.44-he1b5a44_0 perl-archive-tar bioconda/linux-64::perl-archive-tar-2.32-pl526_0 perl-base bioconda/linux-64::perl-base-2.23-pl526_1 perl-common-sense bioconda/linux-64::perl-common-sense-3.74-pl526_2 perl-compress-raw~ bioconda/linux-64::perl-compress-raw-bzip2-2.087-pl526he1b5a44_0 perl-compress-raw~ bioconda/linux-64::perl-compress-raw-zlib-2.087-pl526hc9558a2_0 perl-digest-hmac bioconda/linux-64::perl-digest-hmac-1.03-pl526_3 perl-digest-md5 bioconda/linux-64::perl-digest-md5-2.55-pl526_0 perl-encode-locale bioconda/linux-64::perl-encode-locale-1.05-pl526_6 perl-exporter-tiny bioconda/linux-64::perl-exporter-tiny-1.002001-pl526_0 perl-file-listing bioconda/linux-64::perl-file-listing-6.04-pl526_1 perl-html-parser bioconda/linux-64::perl-html-parser-3.72-pl526h6bb024c_5 perl-html-tagset bioconda/linux-64::perl-html-tagset-3.20-pl526_3 perl-html-tree bioconda/linux-64::perl-html-tree-5.07-pl526_1 perl-http-cookies bioconda/linux-64::perl-http-cookies-6.04-pl526_0 perl-http-daemon bioconda/linux-64::perl-http-daemon-6.01-pl526_1 perl-http-date bioconda/linux-64::perl-http-date-6.02-pl526_3 perl-http-message bioconda/linux-64::perl-http-message-6.18-pl526_0 perl-http-negotia~ bioconda/linux-64::perl-http-negotiate-6.01-pl526_3 perl-io-compress bioconda/linux-64::perl-io-compress-2.087-pl526he1b5a44_0 perl-io-html bioconda/linux-64::perl-io-html-1.001-pl526_2 perl-io-socket-ssl bioconda/linux-64::perl-io-socket-ssl-2.066-pl526_0 perl-io-zlib bioconda/linux-64::perl-io-zlib-1.10-pl526_2 perl-json bioconda/linux-64::perl-json-4.02-pl526_0 perl-json-xs bioconda/linux-64::perl-json-xs-2.34-pl526h6bb024c_3 perl-libwww-perl bioconda/noarch::perl-libwww-perl-6.39-pl526_0 perl-list-moreuti~ bioconda/linux-64::perl-list-moreutils-0.428-pl526_1 perl-list-moreuti~ bioconda/linux-64::perl-list-moreutils-xs-0.428-pl526_0 perl-lwp-mediatyp~ bioconda/linux-64::perl-lwp-mediatypes-6.04-pl526_0 perl-lwp-protocol~ bioconda/linux-64::perl-lwp-protocol-https-6.07-pl526_4 perl-mozilla-ca bioconda/linux-64::perl-mozilla-ca-20180117-pl526_1 perl-net-http bioconda/noarch::perl-net-http-6.19-pl526_0 perl-net-ssleay bioconda/linux-64::perl-net-ssleay-1.88-pl526h90d6eec_0 perl-ntlm bioconda/linux-64::perl-ntlm-1.09-pl526_4 perl-pathtools bioconda/linux-64::perl-pathtools-3.75-pl526h14c3975_1 perl-scalar-list-~ bioconda/linux-64::perl-scalar-list-utils-1.52-pl526h516909a_0 perl-socket bioconda/linux-64::perl-socket-2.027-pl526_1 perl-storable bioconda/linux-64::perl-storable-3.15-pl526h14c3975_0 perl-test-require~ bioconda/linux-64::perl-test-requiresinternet-0.05-pl526_0 perl-time-local bioconda/linux-64::perl-time-local-1.28-pl526_1 perl-try-tiny bioconda/linux-64::perl-try-tiny-0.30-pl526_1 perl-types-serial~ bioconda/linux-64::perl-types-serialiser-1.0-pl526_2 perl-www-robotrul~ bioconda/linux-64::perl-www-robotrules-6.02-pl526_3 perl-xml-parser bioconda/linux-64::perl-xml-parser-2.44-pl526h4e0c4b3_7 perl-xml-sax-expat bioconda/linux-64::perl-xml-sax-expat-0.51-pl526_3 perl-xml-simple bioconda/linux-64::perl-xml-simple-2.25-pl526_1 popt bioconda/linux-64::popt-1.16-1 rsync conda-forge/linux-64::rsync-3.1.3-h1245774_1003 tar conda-forge/linux-64::tar-1.32-hd4ba37b_0 Proceed ([y]/n)?]]> Jit https://bioinformaticsonline.com/snippets/view/42546/install-assembly-stats-with-conda Tue, 05 Jan 2021 04:24:54 -0600 https://bioinformaticsonline.com/snippets/view/42546/install-assembly-stats-with-conda (JitMetaENV) ➜ META_PE conda install -c bioconda assembly-stats Collecting package metadata (current_repodata.json): done Solving environment: done ==> WARNING: A newer version of conda exists. <== current version: 4.9.0 latest version: 4.9.2 Please update conda by running $ conda update -n base -c defaults conda ## Package Plan ## environment location: /home/urbe/anaconda3/envs/JitMetaENV added / updated specs: - assembly-stats The following packages will be downloaded: package | build ---------------------------|----------------- assembly-stats-1.0.1 | hc9558a2_3 29 KB bioconda ------------------------------------------------------------ Total: 29 KB The following NEW packages will be INSTALLED: assembly-stats bioconda/linux-64::assembly-stats-1.0.1-hc9558a2_3 Proceed ([y]/n)?]]> Jit https://bioinformaticsonline.com/snippets/view/42544/install-spades-using-conda Tue, 05 Jan 2021 02:54:37 -0600 https://bioinformaticsonline.com/snippets/view/42544/install-spades-using-conda (JitMetaENV) ➜ fastQC_out conda install -c bioconda spades Collecting package metadata (current_repodata.json): done Solving environment: done ==> WARNING: A newer version of conda exists. <== current version: 4.9.0 latest version: 4.9.2 Please update conda by running $ conda update -n base -c defaults conda ## Package Plan ## environment location: /home/urbe/anaconda3/envs/JitMetaENV added / updated specs: - spades The following packages will be downloaded: package | build ---------------------------|----------------- bzip2-1.0.8 | h7f98852_4 484 KB conda-forge spades-3.14.1 | h2d02072_0 12.7 MB bioconda ------------------------------------------------------------ Total: 13.2 MB The following NEW packages will be INSTALLED: bzip2 conda-forge/linux-64::bzip2-1.0.8-h7f98852_4 llvm-openmp conda-forge/linux-64::llvm-openmp-8.0.1-hc9558a2_0 openmp conda-forge/linux-64::openmp-8.0.1-0 spades bioconda/linux-64::spades-3.14.1-h2d02072_0 Proceed ([y]/n)?]]> Jit