https://bioinformaticsonline.com/snippets?offset=170 https://bioinformaticsonline.com/snippets/view/42920/perl-script-to-run-awk-inside-perl Sat, 27 Feb 2021 01:40:25 -0600 https://bioinformaticsonline.com/snippets/view/42920/perl-script-to-run-awk-inside-perl #!/usr/local/bin/perl eval 'exec /usr/local/bin/perl -S $0 ${1+"$@"}' if $running_under_some_shell; # this emulates #! processing on NIH machines. # (remove #! line above if indigestible) eval '$'.$1.'$2;' while $ARGV[0] =~ /^([A-Za-z_0-9]+=)(.*)/ && shift; # process any FOO=bar switches $, = ' '; # set output field separator $\ = "\n"; # set output record separator while (<>) { chomp; # strip record separator @Fld = split(' ', $_, -1); if ($awk) { $Fld[(1)-1] = ''; $Fld[(2)-1] = ''; print join($,,@Fld); } print join($,,@Fld) if $f1 . . $txt; }]]> Neel https://bioinformaticsonline.com/snippets/view/42919/perl-ipcopen2-module Sat, 27 Feb 2021 01:29:04 -0600 https://bioinformaticsonline.com/snippets/view/42919/perl-ipcopen2-module syntax: $output = open2(\*CHLD_OUT, \*CHLD_IN, 'command arg1 arg2'); It runs a process for both reading and writing and creates a pipe to both STDIN and STDOUT. It can be used in both ways: $output = open2(my $out, my $in, 'command arg1 arg2'); OR without using the shell $output = open2(my $out, my $in, 'command', 'arg1', 'arg2'); You can read about it more in the documentation: IPC::Open2.]]> Neel https://bioinformaticsonline.com/snippets/view/42909/perl-script-to-get-all-the-descendent-in-a-tree Tue, 23 Feb 2021 11:56:59 -0600 https://bioinformaticsonline.com/snippets/view/42909/perl-script-to-get-all-the-descendent-in-a-tree use warnings; use Bio::DB::Taxonomy; #Rotifera 10190 # Get one from a NCBI taxonomy database my $dbh = Bio::DB::Taxonomy->new(-source => 'flatfile', -directory=> "taxdump", -nodesfile=> "taxdump/nodes.dmp", -namesfile=> "taxdump/names.dmp"); my $taxon = $dbh->get_taxon(-taxonid => 10190); my @taxa = $dbh->get_all_Descendents($taxon); foreach (@taxa) {print $_->id; print "\n";}]]> LEGE https://bioinformaticsonline.com/snippets/view/42892/parse-the-ncbi-taxonomy-database-with-perl Wed, 17 Feb 2021 21:17:15 -0600 https://bioinformaticsonline.com/snippets/view/42892/parse-the-ncbi-taxonomy-database-with-perl use Bio::DB::Taxonomy; use warnings; my $sps="human"; # Get one from a NCBI taxonomy database my $dbh = Bio::DB::Taxonomy->new(-source => 'flatfile', -directory=> "taxdump", -nodesfile=> "taxdump/nodes.dmp", -namesfile=> "taxdump/names.dmp"); #to check #parseTax('homo_sapiens', 'metazoa'); #exit; #my $nam = $dbh->get_taxon(-name => $sps); $nam = $dbh->get_taxon(-taxonid => 9606); if(!$nam) { print "Try again with correct scientific name\n"; exit;} print "Eureka we found $sps, id is ", $nam->id, "\n"; # 9606 #$abc = $names{$speciesId}; my @taxa = $dbh->each_Descendent($nam); #foreach (@taxa) {print $_->scientific_name ; print "--";} my @taxa2 = $dbh->get_all_Descendents($nam); #foreach (@taxa2) {print $_->scientific_name; print "**";} #my $ancestor_taxon = $dbh->ancestor($nam); print "$ancestor_taxon->id ****"; #my $tree = $dbh->get_tree('human'); print $tree->name; #print $nam->ancestor; my $ancestor_taxon = $dbh->ancestor($nam); #print $ancestor_taxon; use Bio::Tree::Tree; my $tree_functions = Bio::Tree::Tree->new(); my @lineage = $tree_functions->get_lineage_nodes($nam); my $lineage = $tree_functions->get_lineage_string($nam); #print $lineage; foreach (@lineage) {print $_->scientific_name; print "\n";} my $decision =recheck_class (1974465, "metazoa"); print $decision; #It return 1 of matches otherwise 0 #case-insesitive #Spelling mistake on classNode may leads to error sub recheck_class { my ($lineageId,$classNode)=@_; use Bio::Tree::Tree; my $tree_functions = Bio::Tree::Tree->new(); my $nam = $dbh->get_taxon(-taxonid => $lineageId); my @lineage = $tree_functions->get_lineage_nodes($nam); return 1 if ( grep { lc ($_->scientific_name) eq lc ($classNode)} @lineage ) }]]> LEGE https://bioinformaticsonline.com/snippets/view/42878/install-atom-editor-on-elemantory-os-ubuntu Sun, 14 Feb 2021 12:04:27 -0600 https://bioinformaticsonline.com/snippets/view/42878/install-atom-editor-on-elemantory-os-ubuntu #Download ATOM deb file from https://atom.io/ https://atom.io/download/deb (base) bioqueen@bioqueen-Lenovo-ideapad-320-15ISK:~/Downloads/$ sudo apt install ./atom-amd64.deb [sudo] password for bioqueen: Reading package lists... Done Building dependency tree Reading state information... Done Note, selecting 'atom' instead of './../atom-amd64.deb' The following packages were automatically installed and are no longer required: gir1.2-vte-2.91 libido3-0.1-0 libllvm6.0 libwayland-egl1-mesa Use 'sudo apt autoremove' to remove them. The following additional packages will be installed: gconf-service gconf-service-backend gconf2-common libgconf-2-4 The following NEW packages will be installed: atom gconf-service gconf-service-backend gconf2-common libgconf-2-4 0 upgraded, 5 newly installed, 0 to remove and 0 not upgraded. Need to get 845 kB/127 MB of archives. After this operation, 698 MB 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 gconf2-common all 3.2.6-4ubuntu1 [700 kB] Get:2 http://in.archive.ubuntu.com/ubuntu bionic/universe amd64 libgconf-2-4 amd64 3.2.6-4ubuntu1 [84.8 kB] Get:3 http://in.archive.ubuntu.com/ubuntu bionic/universe amd64 gconf-service-backend amd64 3.2.6-4ubuntu1 [58.1 kB] Get:4 http://in.archive.ubuntu.com/ubuntu bionic/universe amd64 gconf-service amd64 3.2.6-4ubuntu1 [2,036 B] Get:5 /home/bioqueen/Downloads/atom-amd64.deb atom amd64 1.54.0 [126 MB] Fetched 845 kB in 4s (219 kB/s) Selecting previously unselected package gconf2-common. (Reading database ... 194272 files and directories currently installed.) Preparing to unpack .../gconf2-common_3.2.6-4ubuntu1_all.deb ... Unpacking gconf2-common (3.2.6-4ubuntu1) ... Selecting previously unselected package libgconf-2-4:amd64. Preparing to unpack .../libgconf-2-4_3.2.6-4ubuntu1_amd64.deb ... Unpacking libgconf-2-4:amd64 (3.2.6-4ubuntu1) ... Selecting previously unselected package atom. Preparing to unpack .../bioqueen/Downloads/atom-amd64.deb ... Unpacking atom (1.54.0) ... Selecting previously unselected package gconf-service-backend. Preparing to unpack .../gconf-service-backend_3.2.6-4ubuntu1_amd64.deb ... Unpacking gconf-service-backend (3.2.6-4ubuntu1) ... Selecting previously unselected package gconf-service. Preparing to unpack .../gconf-service_3.2.6-4ubuntu1_amd64.deb ... Unpacking gconf-service (3.2.6-4ubuntu1) ... Setting up gconf2-common (3.2.6-4ubuntu1) ... Creating config file /etc/gconf/2/path with new version Setting up libgconf-2-4:amd64 (3.2.6-4ubuntu1) ... Setting up atom (1.54.0) ... Setting up gconf-service-backend (3.2.6-4ubuntu1) ... Setting up gconf-service (3.2.6-4ubuntu1) ... Processing triggers for bamfdaemon (0.5.3+18.04.20180207.2-0ubuntu1) ... Rebuilding /usr/share/applications/bamf-2.index... Processing triggers for libc-bin (2.27-3ubuntu1.4) ... Processing triggers for gnome-menus (3.13.3-11ubuntu1.1) ... Processing triggers for mime-support (3.60ubuntu1) ... Processing triggers for desktop-file-utils (0.23-1ubuntu3.18.04.2+elementary2~ubuntu5.0.1) ... #Now you can add packages in it (base) bioqueen@bioqueen-Lenovo-ideapad-320-15ISK:~/Downloads/$ apm apm - Atom Package Manager powered by https://atom.io Usage: apm <command> where <command> is one of: ci, clean, config, dedupe, deinstall, delete, dev, develop, disable, docs, enable, erase, featured, home, i, init, install, link, linked, links, list, ln, lns, login, ls, open, outdated, prune, publish, rebuild, rebuild-module-cache, remove, rm, search, show, star, starred, stars, test, uninstall, unlink, unpublish, unstar, update, upgrade, view. Run `apm help <command>` to see the more details about a specific command. Options: --color Enable colored output [boolean] [default: true] -v, --version Print the apm version -h, --help Print this usage message Prefix an option with `no-` to set it to false such as --no-color to disable colored output. #Atom is essentially a text editor that you can use for coding. But did you know that you can turn Atom into a full-fledged IDE (integrated development environment) like Eclipse, PyCharm or IntelliJ IDEA etc? (base) bioqueen@bioqueen-Lenovo-ideapad-320-15ISK:~/Downloads/$ apm install atom-ide-ui Installing atom-ide-ui to /home/bioqueen/.atom/packages ✓]]> BioQueen https://bioinformaticsonline.com/snippets/view/42873/converting-from-windows-style-to-unix-style-line-endings-with-dos2unix Sat, 13 Feb 2021 11:24:41 -0600 https://bioinformaticsonline.com/snippets/view/42873/converting-from-windows-style-to-unix-style-line-endings-with-dos2unix Lenovo-ideapad-320-15ISK:~/Downloads/abc/bin$ sudo apt install dos2unix [sudo] password for bioqueen: Reading package lists... Done Building dependency tree Reading state information... Done The following packages were automatically installed and are no longer required: gir1.2-vte-2.91 libido3-0.1-0 libllvm6.0 libwayland-egl1-mesa Use 'sudo apt autoremove' to remove them. The following NEW packages will be installed: dos2unix 0 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. Need to get 351 kB of archives. After this operation, 1,267 kB of additional disk space will be used. Get:1 http://in.archive.ubuntu.com/ubuntu bionic/universe amd64 dos2unix amd64 7.3.4-3 [351 kB] Fetched 351 kB in 3s (130 kB/s) Selecting previously unselected package dos2unix. (Reading database ... 177704 files and directories currently installed.) Preparing to unpack .../dos2unix_7.3.4-3_amd64.deb ... Unpacking dos2unix (7.3.4-3) ... Setting up dos2unix (7.3.4-3) ... Processing triggers for man-db (2.8.3-2ubuntu0.1) ...]]> BioQueen https://bioinformaticsonline.com/snippets/view/42820/steps-to-install-conda-on-linux Mon, 08 Feb 2021 01:11:44 -0600 https://bioinformaticsonline.com/snippets/view/42820/steps-to-install-conda-on-linux Download the installer: Miniconda installer for Linux. ( https://docs.conda.io/en/latest/miniconda.html#linux-installers ) Anaconda installer for Linux. ( https://www.anaconda.com/products/individual ) $ chmod 777 Anaconda3-2020.11-Linux-x86_64.sh $ ./Anaconda3-2020.11-Linux-x86_64.sh #Follow the yes/no flags and finish till the end #Check the installation $ conda -V A few other frequently used commands # list all the conda environment available conda info --envs # Create new environment named as `envname` conda create --name envname # Remove environment and its dependencies conda remove --name envname --all # Clone an existing environment conda create --name clone_envname --clone envname]]> BioStar https://bioinformaticsonline.com/snippets/view/42656/command-to-create-conda-environment Thu, 21 Jan 2021 04:39:56 -0600 https://bioinformaticsonline.com/snippets/view/42656/command-to-create-conda-environment # using pip pip install -r requirements.txt # using Conda conda create --name <env_name> --file requirements.txt #Using yaml conda env create -f environment.yml #Listing env conda env list #Create env with python36 conda create -n myenv python=3.6]]> Neel https://bioinformaticsonline.com/snippets/view/42642/install-and-set-up-i-adhore-for-synteny-and-wgd-analysis-step-by-step Sun, 17 Jan 2021 21:32:34 -0600 https://bioinformaticsonline.com/snippets/view/42642/install-and-set-up-i-adhore-for-synteny-and-wgd-analysis-step-by-step #Need to download i-adhore-3.0.01.tar.gz from https://wdiceryfd4rjn74bjhhtz2k5di--bioinformatics-psb-ugent-be.translate.goog/webtools/i-adhore/licensing/ #Follow these steps (wgd) ➜ i-adhore-3.0.01 git:(master) ✗ tar -zxvf i-adhore-3.0.01.tar.gz (wgd) ➜ i-adhore-3.0.01 git:(master) ✗ cd i-adhore-3.0.01 (wgd) ➜ i-adhore-3.0.01 git:(master) ✗ mkdir -p build && cd build (wgd) ➜ build git:(master) ✗ which wgd /home/urbe/anaconda3/envs/wgd/bin/wgd (wgd) ➜ build git:(master) ✗ cmake .. -DCMAKE_INSTALL_PREFIX=/home/urbe/anaconda3/envs/wgd/ CMake Deprecation Warning at CMakeLists.txt:2 (cmake_minimum_required): Compatibility with CMake < 2.8.12 will be removed from a future version of CMake. Update the VERSION argument <min> value or use a ...<max> suffix to tell CMake that the project does not need compatibility with older versions. -- The C compiler identification is GNU 7.5.0 -- The CXX compiler identification is GNU 7.5.0 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /usr/bin/cc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/c++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- Looking for pthread.h -- Looking for pthread.h - found -- Performing Test CMAKE_HAVE_LIBC_PTHREAD -- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Failed -- Looking for pthread_create in pthreads -- Looking for pthread_create in pthreads - not found -- Looking for pthread_create in pthread -- Looking for pthread_create in pthread - found -- Found Threads: TRUE -- Found MPI_C: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so (found version "3.1") -- Found MPI_CXX: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_cxx.so (found version "3.1") -- Found MPI: TRUE (found version "3.1") -- Found ZLIB: /usr/lib/x86_64-linux-gnu/libz.so (found version "1.2.11") -- Found PNG: /usr/lib/x86_64-linux-gnu/libpng.so (found version "1.6.34") -- Configuring done -- Generating done -- Build files have been written to: /home/urbe/Tools/i-adhore-3.0.01/build (wgd) ➜ build git:(master) ✗ ls CMakeCache.txt CMakeFiles cmake_install.cmake Makefile src unittest (wgd) ➜ build git:(master) ✗ make -j 4 Scanning dependencies of target bmp Scanning dependencies of target alignment [ 3%] Building CXX object src/bmp/CMakeFiles/bmp.dir/bmp.cpp.o [ 3%] Building CXX object src/bmp/CMakeFiles/bmp.dir/grafix.cpp.o [ 4%] Building CXX object src/bmp/CMakeFiles/bmp.dir/color.cpp.o [ 6%] Building CXX object src/alignment/CMakeFiles/alignment.dir/GGAligner.cpp.o [ 8%] Building CXX object src/bmp/CMakeFiles/bmp.dir/pnghandling.cpp.o [ 9%] Building CXX object src/alignment/CMakeFiles/alignment.dir/GGAligner2.cpp.o [ 13%] Building CXX object src/alignment/CMakeFiles/alignment.dir/NWAligner.cpp.o [ 13%] Linking CXX static library libbmp.a [ 13%] Built target bmp [ 14%] Building CXX object src/alignment/CMakeFiles/alignment.dir/Node.cpp.o [ 16%] Linking CXX static library libalignment.a [ 16%] Built target alignment Scanning dependencies of target i-adhore Scanning dependencies of target i-visualize [ 18%] Building CXX object src/CMakeFiles/i-visualize.dir/PostProcessor.cpp.o [ 21%] Building CXX object src/CMakeFiles/i-visualize.dir/AlignmentVisualizer.cpp.o [ 21%] Building CXX object src/CMakeFiles/i-visualize.dir/threadPool.cpp.o [ 22%] Building CXX object src/CMakeFiles/i-adhore.dir/threadPool.cpp.o [ 24%] Building CXX object src/CMakeFiles/i-visualize.dir/higherLevel.cpp.o [ 26%] Building CXX object src/CMakeFiles/i-adhore.dir/higherLevel.cpp.o [ 27%] Building CXX object src/CMakeFiles/i-visualize.dir/levelTwo.cpp.o [ 29%] Building CXX object src/CMakeFiles/i-visualize.dir/alignComp.cpp.o [ 31%] Building CXX object src/CMakeFiles/i-visualize.dir/SvgWriter.cpp.o [ 32%] Building CXX object src/CMakeFiles/i-adhore.dir/levelTwo.cpp.o /home/urbe/Tools/i-adhore-3.0.01/src/SvgWriter.cpp: In member function ‘std::__cxx11::string SvgWriter::convertColor(const Color&)’: /home/urbe/Tools/i-adhore-3.0.01/src/SvgWriter.cpp:24:8: warning: ‘%x’ directive writing 1 byte into a region of size between 0 and 6 [-Wformat-overflow=] string SvgWriter::convertColor(const Color& color) ^~~~~~~~~ /home/urbe/Tools/i-adhore-3.0.01/src/SvgWriter.cpp:24:8: note: directive argument in the range [0, 15] /home/urbe/Tools/i-adhore-3.0.01/src/SvgWriter.cpp:24:8: note: directive argument in the range [0, 268435455] /home/urbe/Tools/i-adhore-3.0.01/src/SvgWriter.cpp:24:8: note: directive argument in the range [0, 15] /home/urbe/Tools/i-adhore-3.0.01/src/SvgWriter.cpp:24:8: note: directive argument in the range [0, 268435455] /home/urbe/Tools/i-adhore-3.0.01/src/SvgWriter.cpp:24:8: note: directive argument in the range [0, 15] In file included from /usr/include/stdio.h:862:0, from /usr/include/c++/7/cstdio:42, from /usr/include/c++/7/ext/string_conversions.h:43, from /usr/include/c++/7/bits/basic_string.h:6361, from /usr/include/c++/7/string:52, from /usr/include/c++/7/bits/locale_classes.h:40, from /usr/include/c++/7/bits/ios_base.h:41, from /usr/include/c++/7/ios:42, from /usr/include/c++/7/ostream:38, from /usr/include/c++/7/iostream:39, from /home/urbe/Tools/i-adhore-3.0.01/src/SvgWriter.h:4, from /home/urbe/Tools/i-adhore-3.0.01/src/SvgWriter.cpp:1: /usr/include/x86_64-linux-gnu/bits/stdio2.h:34:43: note: ‘__builtin___sprintf_chk’ output between 8 and 26 bytes into a destination of size 8 __bos (__s), __fmt, __va_arg_pack ()); ^ [ 34%] Building CXX object src/CMakeFiles/i-visualize.dir/AlignmentDrawer.cpp.o [ 36%] Building CXX object src/CMakeFiles/i-visualize.dir/parallel.cpp.o [ 37%] Building CXX object src/CMakeFiles/i-adhore.dir/alignComp.cpp.o [ 39%] Building CXX object src/CMakeFiles/i-visualize.dir/SynthenicCloud.cpp.o [ 40%] Building CXX object src/CMakeFiles/i-adhore.dir/SvgWriter.cpp.o [ 42%] Building CXX object src/CMakeFiles/i-adhore.dir/AlignmentDrawer.cpp.o [ 44%] Building CXX object src/CMakeFiles/i-adhore.dir/parallel.cpp.o /home/urbe/Tools/i-adhore-3.0.01/src/SvgWriter.cpp: In member function ‘std::__cxx11::string SvgWriter::convertColor(const Color&)’: /home/urbe/Tools/i-adhore-3.0.01/src/SvgWriter.cpp:24:8: warning: ‘%x’ directive writing 1 byte into a region of size between 0 and 6 [-Wformat-overflow=] string SvgWriter::convertColor(const Color& color) ^~~~~~~~~ /home/urbe/Tools/i-adhore-3.0.01/src/SvgWriter.cpp:24:8: note: directive argument in the range [0, 15] /home/urbe/Tools/i-adhore-3.0.01/src/SvgWriter.cpp:24:8: note: directive argument in the range [0, 268435455] /home/urbe/Tools/i-adhore-3.0.01/src/SvgWriter.cpp:24:8: note: directive argument in the range [0, 15] /home/urbe/Tools/i-adhore-3.0.01/src/SvgWriter.cpp:24:8: note: directive argument in the range [0, 268435455] /home/urbe/Tools/i-adhore-3.0.01/src/SvgWriter.cpp:24:8: note: directive argument in the range [0, 15] In file included from /usr/include/stdio.h:862:0, from /usr/include/c++/7/cstdio:42, from /usr/include/c++/7/ext/string_conversions.h:43, from /usr/include/c++/7/bits/basic_string.h:6361, from /usr/include/c++/7/string:52, from /usr/include/c++/7/bits/locale_classes.h:40, from /usr/include/c++/7/bits/ios_base.h:41, from /usr/include/c++/7/ios:42, from /usr/include/c++/7/ostream:38, from /usr/include/c++/7/iostream:39, from /home/urbe/Tools/i-adhore-3.0.01/src/SvgWriter.h:4, from /home/urbe/Tools/i-adhore-3.0.01/src/SvgWriter.cpp:1: /usr/include/x86_64-linux-gnu/bits/stdio2.h:34:43: note: ‘__builtin___sprintf_chk’ output between 8 and 26 bytes into a destination of size 8 __bos (__s), __fmt, __va_arg_pack ()); ^ [ 45%] Building CXX object src/CMakeFiles/i-visualize.dir/BaseCluster.cpp.o [ 47%] Building CXX object src/CMakeFiles/i-adhore.dir/SynthenicCloud.cpp.o [ 49%] Building CXX object src/CMakeFiles/i-adhore.dir/BaseCluster.cpp.o [ 50%] Building CXX object src/CMakeFiles/i-adhore.dir/Cluster.cpp.o [ 52%] Building CXX object src/CMakeFiles/i-adhore.dir/DataSet.cpp.o [ 54%] Building CXX object src/CMakeFiles/i-visualize.dir/Cluster.cpp.o [ 55%] Building CXX object src/CMakeFiles/i-adhore.dir/GHM.cpp.o [ 57%] Building CXX object src/CMakeFiles/i-visualize.dir/DataSet.cpp.o [ 59%] Building CXX object src/CMakeFiles/i-adhore.dir/GHMProfile.cpp.o /home/urbe/Tools/i-adhore-3.0.01/src/DataSet.cpp: In member function ‘void DataSet::prepareOutput()’: /home/urbe/Tools/i-adhore-3.0.01/src/DataSet.cpp:306:11: warning: ignoring return value of ‘int system(const char*)’, declared with attribute warn_unused_result [-Wunused-result] system(command.append(outputPath).c_str()); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/urbe/Tools/i-adhore-3.0.01/src/DataSet.cpp: In member function ‘void DataSet::prepareOutput()’: /home/urbe/Tools/i-adhore-3.0.01/src/DataSet.cpp:306:11: warning: ignoring return value of ‘int system(const char*)’, declared with attribute warn_unused_result [-Wunused-result] system(command.append(outputPath).c_str()); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 60%] Building CXX object src/CMakeFiles/i-visualize.dir/GHM.cpp.o [ 62%] Building CXX object src/CMakeFiles/i-adhore.dir/Gene.cpp.o [ 63%] Building CXX object src/CMakeFiles/i-visualize.dir/GHMProfile.cpp.o [ 65%] Building CXX object src/CMakeFiles/i-adhore.dir/GeneFamily.cpp.o [ 67%] Building CXX object src/CMakeFiles/i-adhore.dir/GeneList.cpp.o [ 68%] Building CXX object src/CMakeFiles/i-visualize.dir/Gene.cpp.o [ 70%] Building CXX object src/CMakeFiles/i-adhore.dir/GenePairs.cpp.o [ 72%] Building CXX object src/CMakeFiles/i-adhore.dir/ListElement.cpp.o [ 73%] Building CXX object src/CMakeFiles/i-visualize.dir/GeneFamily.cpp.o [ 75%] Building CXX object src/CMakeFiles/i-visualize.dir/GeneList.cpp.o [ 77%] Building CXX object src/CMakeFiles/i-adhore.dir/Multiplicon.cpp.o [ 78%] Building CXX object src/CMakeFiles/i-adhore.dir/Profile.cpp.o [ 80%] Building CXX object src/CMakeFiles/i-visualize.dir/GenePairs.cpp.o [ 81%] Building CXX object src/CMakeFiles/i-adhore.dir/Settings.cpp.o [ 83%] Building CXX object src/CMakeFiles/i-adhore.dir/iADHoRe.cpp.o [ 85%] Building CXX object src/CMakeFiles/i-visualize.dir/ListElement.cpp.o [ 86%] Building CXX object src/CMakeFiles/i-adhore.dir/hpmath.cpp.o [ 88%] Building CXX object src/CMakeFiles/i-adhore.dir/util.cpp.o [ 90%] Building CXX object src/CMakeFiles/i-visualize.dir/Multiplicon.cpp.o [ 91%] Building CXX object src/CMakeFiles/i-visualize.dir/Profile.cpp.o [ 93%] Building CXX object src/CMakeFiles/i-visualize.dir/Settings.cpp.o [ 95%] Linking CXX executable i-adhore [ 95%] Built target i-adhore [ 96%] Building CXX object src/CMakeFiles/i-visualize.dir/hpmath.cpp.o [ 98%] Building CXX object src/CMakeFiles/i-visualize.dir/util.cpp.o [100%] Linking CXX executable i-visualize [100%] Built target i-visualize (wgd) ➜ build git:(master) ✗ make install [ 8%] Built target bmp [ 16%] Built target alignment [ 59%] Built target i-visualize [100%] Built target i-adhore Install the project... -- Install configuration: "Release" -- Installing: /home/urbe/anaconda3/envs/wgd/./API -- Installing: /home/urbe/anaconda3/envs/wgd/./API/iADHoRe -- Installing: /home/urbe/anaconda3/envs/wgd/./API/iADHoRe/central.pm -- Installing: /home/urbe/anaconda3/envs/wgd/./API/iADHoRe/record_structure.pm -- Installing: /home/urbe/anaconda3/envs/wgd/./API/iADHoRe/list_element.pm -- Installing: /home/urbe/anaconda3/envs/wgd/./API/iADHoRe/settings.pm -- Installing: 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/home/urbe/anaconda3/envs/wgd/./testset/datasetI/arath_2_3_beta/baseclusters.txt -- Installing: /home/urbe/anaconda3/envs/wgd/./testset/datasetI/arath_2_3_beta/cloudAP.txt -- Installing: /home/urbe/anaconda3/envs/wgd/./testset/datasetI/arath_2_3_beta/multiplicons.txt -- Installing: /home/urbe/anaconda3/envs/wgd/./testset/datasetI/arath_2_3_beta/segments.txt -- Installing: /home/urbe/anaconda3/envs/wgd/./testset/datasetI/arath_2_3_beta/alignment.txt -- Installing: /home/urbe/anaconda3/envs/wgd/./testset/datasetI/i-visualize -- Installing: /home/urbe/anaconda3/envs/wgd/./testset/datasetI/ath_lists -- Installing: /home/urbe/anaconda3/envs/wgd/./testset/datasetI/ath_lists/1.lst -- Installing: /home/urbe/anaconda3/envs/wgd/./testset/datasetI/ath_lists/2.lst -- Installing: /home/urbe/anaconda3/envs/wgd/./testset/datasetI/ath_lists/3.lst -- Installing: /home/urbe/anaconda3/envs/wgd/./testset/datasetI/ath_lists/5.lst -- Installing: /home/urbe/anaconda3/envs/wgd/./testset/datasetI/ath_lists/4.lst -- Installing: /home/urbe/anaconda3/envs/wgd/./testset/datasetI/families.csv -- Installing: /home/urbe/anaconda3/envs/wgd/./testset/datasetI/datasetI.ini -- Installing: /home/urbe/anaconda3/envs/wgd/bin/i-adhore -- Set runtime path of "/home/urbe/anaconda3/envs/wgd/bin/i-adhore" to "" -- Installing: /home/urbe/anaconda3/envs/wgd/bin/i-visualize -- Set runtime path of "/home/urbe/anaconda3/envs/wgd/bin/i-visualize" to ""]]> Jit https://bioinformaticsonline.com/snippets/view/42640/set-up-wgd-environment-using-conda Sun, 17 Jan 2021 19:24:15 -0600 https://bioinformaticsonline.com/snippets/view/42640/set-up-wgd-environment-using-conda #Wgd cannot be installed directly with bioconda at present, so it is slightly troublesome to install, because it #depends on a lot of software. wgd depends on the following software #BLAST #MCL #MUSCLE/MAFFT/PRANK #PAML #PhyML/FastTree #i-ADHoRe #Creat the conda ENV and install its deps #Follow the steps (base) ➜ wgd git:(master) conda create -n wgd python=3.7 blast mcl muscle mafft prank paml fasttree cmake libpng mpi=1.0=mpich 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/anaconda3/envs/wgd added / updated specs: - blast - cmake - fasttree - libpng - mafft - mcl - mpi==1.0=mpich - muscle - paml - prank - python=3.7 The following packages will be downloaded: package | build ---------------------------|----------------- boost-1.74.0 | py37he5a615d_2 335 KB conda-forge boost-cpp-1.74.0 | h9d3c048_1 16.3 MB conda-forge c-ares-1.17.1 | h36c2ea0_0 111 KB conda-forge certifi-2020.12.5 | py37h89c1867_1 143 KB conda-forge cmake-3.19.3 | h4547794_0 14.0 MB conda-forge libblas-3.9.0 | 7_openblas 11 KB conda-forge libcblas-3.9.0 | 7_openblas 11 KB conda-forge libgfortran-ng-9.3.0 | hff62375_18 22 KB conda-forge libgfortran5-9.3.0 | hff62375_18 2.0 MB conda-forge liblapack-3.9.0 | 7_openblas 11 KB conda-forge libnghttp2-1.41.0 | h8cfc5f6_2 774 KB conda-forge numpy-1.19.5 | py37haa41c4c_1 5.3 MB conda-forge python-3.7.9 |hffdb5ce_0_cpython 57.3 MB conda-forge setuptools-49.6.0 | py37h89c1867_3 947 KB conda-forge ------------------------------------------------------------ Total: 97.2 MB The following NEW packages will be INSTALLED: _libgcc_mutex conda-forge/linux-64::_libgcc_mutex-0.1-conda_forge _openmp_mutex conda-forge/linux-64::_openmp_mutex-4.5-1_gnu blast bioconda/linux-64::blast-2.5.0-hc0b0e79_3 boost conda-forge/linux-64::boost-1.74.0-py37he5a615d_2 boost-cpp conda-forge/linux-64::boost-cpp-1.74.0-h9d3c048_1 bzip2 conda-forge/linux-64::bzip2-1.0.8-h7f98852_4 c-ares conda-forge/linux-64::c-ares-1.17.1-h36c2ea0_0 ca-certificates conda-forge/linux-64::ca-certificates-2020.12.5-ha878542_0 certifi conda-forge/linux-64::certifi-2020.12.5-py37h89c1867_1 cmake conda-forge/linux-64::cmake-3.19.3-h4547794_0 expat conda-forge/linux-64::expat-2.2.9-he1b5a44_2 fasttree bioconda/linux-64::fasttree-2.1.10-h516909a_4 icu conda-forge/linux-64::icu-68.1-h58526e2_0 krb5 conda-forge/linux-64::krb5-1.17.2-h926e7f8_0 ld_impl_linux-64 conda-forge/linux-64::ld_impl_linux-64-2.35.1-hea4e1c9_1 libblas conda-forge/linux-64::libblas-3.9.0-7_openblas libcblas conda-forge/linux-64::libcblas-3.9.0-7_openblas libcurl conda-forge/linux-64::libcurl-7.71.1-hcdd3856_8 libedit conda-forge/linux-64::libedit-3.1.20191231-he28a2e2_2 libev conda-forge/linux-64::libev-4.33-h516909a_1 libffi conda-forge/linux-64::libffi-3.3-h58526e2_2 libgcc-ng conda-forge/linux-64::libgcc-ng-9.3.0-h2828fa1_18 libgfortran-ng conda-forge/linux-64::libgfortran-ng-9.3.0-hff62375_18 libgfortran5 conda-forge/linux-64::libgfortran5-9.3.0-hff62375_18 libgomp conda-forge/linux-64::libgomp-9.3.0-h2828fa1_18 liblapack conda-forge/linux-64::liblapack-3.9.0-7_openblas libnghttp2 conda-forge/linux-64::libnghttp2-1.41.0-h8cfc5f6_2 libopenblas conda-forge/linux-64::libopenblas-0.3.12-pthreads_h4812303_1 libpng conda-forge/linux-64::libpng-1.6.37-h21135ba_2 libssh2 conda-forge/linux-64::libssh2-1.9.0-hab1572f_5 libstdcxx-ng conda-forge/linux-64::libstdcxx-ng-9.3.0-h6de172a_18 libuv conda-forge/linux-64::libuv-1.40.0-h7f98852_0 lz4-c conda-forge/linux-64::lz4-c-1.9.3-h9c3ff4c_0 mafft bioconda/linux-64::mafft-7.475-h516909a_0 mcl bioconda/linux-64::mcl-14.137-pl526h516909a_5 mpi conda-forge/linux-64::mpi-1.0-mpich muscle bioconda/linux-64::muscle-3.8.1551-hc9558a2_5 ncurses conda-forge/linux-64::ncurses-6.2-h58526e2_4 numpy conda-forge/linux-64::numpy-1.19.5-py37haa41c4c_1 openssl conda-forge/linux-64::openssl-1.1.1i-h7f98852_0 paml bioconda/linux-64::paml-4.9-h516909a_5 perl conda-forge/linux-64::perl-5.26.2-h36c2ea0_1008 pip conda-forge/noarch::pip-20.3.3-pyhd8ed1ab_0 prank bioconda/linux-64::prank-v.170427-hc9558a2_3 python conda-forge/linux-64::python-3.7.9-hffdb5ce_0_cpython python_abi conda-forge/linux-64::python_abi-3.7-1_cp37m readline conda-forge/linux-64::readline-8.0-he28a2e2_2 rhash conda-forge/linux-64::rhash-1.4.1-h7f98852_0 setuptools conda-forge/linux-64::setuptools-49.6.0-py37h89c1867_3 sqlite conda-forge/linux-64::sqlite-3.34.0-h74cdb3f_0 tk conda-forge/linux-64::tk-8.6.10-h21135ba_1 wheel conda-forge/noarch::wheel-0.36.2-pyhd3deb0d_0 xz conda-forge/linux-64::xz-5.2.5-h516909a_1 zlib conda-forge/linux-64::zlib-1.2.11-h516909a_1010 zstd conda-forge/linux-64::zstd-1.4.8-ha95c52a_1 Proceed ([y]/n)? y Downloading and Extracting Packages libgfortran-ng-9.3.0 | 22 KB | ################################################################################ | 100% libnghttp2-1.41.0 | 774 KB | ################################################################################ | 100% libcblas-3.9.0 | 11 KB | ################################################################################ | 100% liblapack-3.9.0 | 11 KB | ################################################################################ | 100% certifi-2020.12.5 | 143 KB | ################################################################################ | 100% cmake-3.19.3 | 14.0 MB | ################################################################################ | 100% libgfortran5-9.3.0 | 2.0 MB | ################################################################################ | 100% c-ares-1.17.1 | 111 KB | ################################################################################ | 100% numpy-1.19.5 | 5.3 MB | ################################################################################ | 100% libblas-3.9.0 | 11 KB | ################################################################################ | 100% python-3.7.9 | 57.3 MB | ################################################################################ | 100% boost-cpp-1.74.0 | 16.3 MB | ################################################################################ | 100% setuptools-49.6.0 | 947 KB | ################################################################################ | 100% boost-1.74.0 | 335 KB | ################################################################################ | 100% Preparing transaction: done Verifying transaction: done Executing transaction: done # # To activate this environment, use # # $ conda activate wgd # # To deactivate an active environment, use # # $ conda deactivate #----------------------------------------------------- set uo wgd (wgd) ➜ Tools git:(master) ✗ git clone https://github.com/arzwa/wgd.git (wgd) ➜ Tools git:(master) ✗ cd wgd (wgd) ➜ wgd git:(master) ls doc example LICENSE README.md setup.py Singularity wgd wgd_cli.py (wgd) ➜ wgd git:(master) pip install . Processing /home/urbe/Tools/wgd Requirement already satisfied: numpy>=1.16 in /home/urbe/anaconda3/envs/wgd/lib/python3.7/site-packages (from wgd==1.2) (1.19.5) Collecting bokeh==1.4.0 Using cached bokeh-1.4.0.tar.gz (32.4 MB) Collecting fastcluster==1.1.25 Downloading fastcluster-1.1.25-cp37-cp37m-manylinux1_x86_64.whl (154 kB) |████████████████████████████████| 154 kB 5.8 MB/s Collecting joblib==0.11 Using cached joblib-0.11-py2.py3-none-any.whl (176 kB) Collecting pandas==0.24.1 Downloading pandas-0.24.1-cp37-cp37m-manylinux1_x86_64.whl (10.1 MB) |████████████████████████████████| 10.1 MB 29 kB/s Collecting biopython>=1.75 Using cached biopython-1.78-cp37-cp37m-manylinux1_x86_64.whl (2.3 MB) Collecting click>=7.0 Using cached click-7.1.2-py2.py3-none-any.whl (82 kB) Collecting coloredlogs>=10.0 Using cached coloredlogs-15.0-py2.py3-none-any.whl (45 kB) Collecting ete3>=3.1 Using cached ete3-3.1.2.tar.gz (4.7 MB) Collecting humanfriendly>=9.1 Using cached humanfriendly-9.1-py2.py3-none-any.whl (86 kB) Collecting Jinja2>=2.7 Using cached Jinja2-2.11.2-py2.py3-none-any.whl (125 kB) Collecting MarkupSafe>=0.23 Using cached MarkupSafe-1.1.1-cp37-cp37m-manylinux1_x86_64.whl (27 kB) Collecting matplotlib>=3.0.2 Downloading matplotlib-3.3.3-cp37-cp37m-manylinux1_x86_64.whl (11.6 MB) |████████████████████████████████| 11.6 MB 29 kB/s Collecting cycler>=0.10 Using cached cycler-0.10.0-py2.py3-none-any.whl (6.5 kB) Collecting kiwisolver>=1.0.1 Downloading kiwisolver-1.3.1-cp37-cp37m-manylinux1_x86_64.whl (1.1 MB) |████████████████████████████████| 1.1 MB 68.0 MB/s Collecting packaging>=16.8 Using cached packaging-20.8-py2.py3-none-any.whl (39 kB) Collecting pillow>=4.0 Downloading Pillow-8.1.0-cp37-cp37m-manylinux1_x86_64.whl (2.2 MB) |████████████████████████████████| 2.2 MB 53.5 MB/s Collecting plumbum>=1.6.7 Using cached plumbum-1.6.9-py2.py3-none-any.whl (115 kB) Collecting progressbar2>=3.39 Using cached progressbar2-3.53.1-py2.py3-none-any.whl (25 kB) Collecting pyparsing!=2.0.4,!=2.1.2,!=2.1.6,>=2.0.3 Using cached pyparsing-2.4.7-py2.py3-none-any.whl (67 kB) Collecting python-dateutil>=2.1 Using cached python_dateutil-2.8.1-py2.py3-none-any.whl (227 kB) Collecting python-utils>=2.3.0 Downloading python_utils-2.5.1-py2.py3-none-any.whl (13 kB) Collecting pytz>=2011k Downloading pytz-2020.5-py2.py3-none-any.whl (510 kB) |████████████████████████████████| 510 kB 38.1 MB/s Collecting PyYAML>=3.10 Using cached PyYAML-5.3.1.tar.gz (269 kB) Collecting scipy>=1.2 Downloading scipy-1.6.0-cp37-cp37m-manylinux1_x86_64.whl (27.4 MB) |████████████████████████████████| 27.4 MB 2.0 kB/s Collecting seaborn>=0.9.0 Using cached seaborn-0.11.1-py3-none-any.whl (285 kB) Collecting six>=1.5.2 Using cached six-1.15.0-py2.py3-none-any.whl (10 kB) Collecting tornado>=4.3 Downloading tornado-6.1-cp37-cp37m-manylinux2010_x86_64.whl (428 kB) |████████████████████████████████| 428 kB 61.8 MB/s Collecting sklearn Using cached sklearn-0.0.tar.gz (1.1 kB) Collecting scikit-learn Downloading scikit_learn-0.24.0-cp37-cp37m-manylinux2010_x86_64.whl (22.3 MB) |████████████████████████████████| 22.3 MB 6.0 kB/s Collecting threadpoolctl>=2.0.0 Using cached threadpoolctl-2.1.0-py3-none-any.whl (12 kB) Building wheels for collected packages: wgd, bokeh, ete3, PyYAML, sklearn Building wheel for wgd (setup.py) ... done Created wheel for wgd: filename=wgd-1.2-py3-none-any.whl size=75291 sha256=56a7a19b3f4e535897038e8297166a640a7a6a7fdfeb89f5afde4aaa0208ae67 Stored in directory: /tmp/pip-ephem-wheel-cache-29m8tx5i/wheels/54/f3/0c/285aa1e33c52ac42d7996c0170a686e47362e33f012b2b3669 Building wheel for bokeh (setup.py) ... done Created wheel for bokeh: filename=bokeh-1.4.0-py3-none-any.whl size=23689200 sha256=7daa115fd1b052d429abb6c7082cbbb96defc81716da99ce873760cedf0dbe6f Stored in directory: /home/urbe/.cache/pip/wheels/49/8c/d1/6b8e1f57e542671673cb3d2faee1a9eccb36be2c08a3915498 Building wheel for ete3 (setup.py) ... done Created wheel for ete3: filename=ete3-3.1.2-py3-none-any.whl size=2272998 sha256=4f8c179d7e30d22661fff06e2be08125d837dcff31d4eac36dfb206639ce693f Stored in directory: /home/urbe/.cache/pip/wheels/17/fd/e2/6ac384d8c2484789304657dde01b96d7ab83f4f1dd96d266df Building wheel for PyYAML (setup.py) ... done Created wheel for PyYAML: filename=PyYAML-5.3.1-cp37-cp37m-linux_x86_64.whl size=44620 sha256=89175438317c730e5db0088255ca2f5a9745368487ed0fd0c7dbf644774c45c0 Stored in directory: /home/urbe/.cache/pip/wheels/5e/03/1e/e1e954795d6f35dfc7b637fe2277bff021303bd9570ecea653 Building wheel for sklearn (setup.py) ... done Created wheel for sklearn: filename=sklearn-0.0-py2.py3-none-any.whl size=1316 sha256=4e2eed235501a23fa4cb58a4faef00b3c824d88a5a6d6b7478d45bdfd09bad6c Stored in directory: /home/urbe/.cache/pip/wheels/46/ef/c3/157e41f5ee1372d1be90b09f74f82b10e391eaacca8f22d33e Successfully built wgd bokeh ete3 PyYAML sklearn Installing collected packages: six, threadpoolctl, scipy, pytz, python-dateutil, pyparsing, pillow, MarkupSafe, kiwisolver, joblib, cycler, tornado, scikit-learn, PyYAML, python-utils, pandas, packaging, matplotlib, Jinja2, humanfriendly, sklearn, seaborn, progressbar2, plumbum, fastcluster, ete3, coloredlogs, click, bokeh, biopython, wgd Successfully installed Jinja2-2.11.2 MarkupSafe-1.1.1 PyYAML-5.3.1 biopython-1.78 bokeh-1.4.0 click-7.1.2 coloredlogs-15.0 cycler-0.10.0 ete3-3.1.2 fastcluster-1.1.25 humanfriendly-9.1 joblib-0.11 kiwisolver-1.3.1 matplotlib-3.3.3 packaging-20.8 pandas-0.24.1 pillow-8.1.0 plumbum-1.6.9 progressbar2-3.53.1 pyparsing-2.4.7 python-dateutil-2.8.1 python-utils-2.5.1 pytz-2020.5 scikit-learn-0.24.0 scipy-1.6.0 seaborn-0.11.1 six-1.15.0 sklearn-0.0 threadpoolctl-2.1.0 tornado-6.1 wgd-1.2 (wgd) ➜ wgd git:(master) wgd zsh: correct 'wgd' to 'gd' [nyae]? n Usage: wgd [OPTIONS] COMMAND [ARGS]... Welcome to the wgd command line interface! _______ \ ___ `'. _ _ .--./) ' |--.\ \ /\ \\ ///.''\\ | | \ ' `\\ //\\ //| | | | | | | ' \`// \'/ \`-' / | | | | \| |/ /("'` | | ' .' ' \ '---. | |___.' /' /'""'.\ /_______.'/ || ||\_______|/ \'. __// `'---' wgd Copyright (C) 2018 Arthur Zwaenepoel This program comes with ABSOLUTELY NO WARRANTY; This is free software, and you are welcome to redistribute it under certain conditions; Contact: arzwa@psb.vib-ugent.be Options: -v, --verbosity [info|debug] Verbosity level, default = info. -l, --logfile TEXT File to write logs to (optional) --version Print version number -h, --help Show this message and exit. Commands: dmd All-vs.-all diamond blastp + MCL clustering. kde Fit a KDE to a Ks distribution. ksd Ks distribution construction. mcl All-vs.-all blastp + MCL clustering. mix Mixture modeling of Ks distributions. pre Check and optionally rename CDS files. syn Co-linearity analyses. viz Plot histograms/densities (interactively). wf1 Standard workflow whole paranome Ks. wf2 Standard workflow one-vs-one ortholog Ks.]]> BioStar