{"action":"created","comment":{"url":"https://api.github.com/repos/biocore/WGS-HGT/pulls/comments/49867480","id":49867480,"diff_hunk":"@@ -0,0 +1,116 @@\n+#!/bin/bash\n+\n+# ----------------------------------------------------------------------------\n+# Copyright (c) 2015--, The WGS-HGT Development Team.\n+#\n+# Distributed under the terms of the Modified BSD License.\n+#\n+# The full license is in the file COPYING.txt, distributed with this software.\n+# ----------------------------------------------------------------------------\n+\n+# This script will preprocess files (determine orthologous genes, compute\n+# their trees and MSAs, run BLASTP on the query genome) and passes this data\n+# to launch_software.sh for executing HGT detection software\n+\n+# working dir\n+working_dir=$(readlink -m $1)\n+# scripts dir\n+scripts_dir=$(readlink -m $2)\n+# species tree in Newick format\n+species_tree_fp=$3\n+# species raw genome in FASTA format\n+species_genome_fp=$4\n+# species HMM model (produced by GeneMarkS)\n+species_model_fp=$5\n+# query species protein coding sequences in FASTA format\n+query_species_coding_seqs_fp=$6\n+# reference species protein coding sequences in FASTA format\n+ref_species_coding_seqs_fp=$7\n+# gene trees in Newick format\n+gene_tree_dir=$8\n+# gene multiple sequence alignment dir\n+gene_msa_dir=$9\n+# tabular DIAMOND alignments of query genome\n+diamond_query_tabular=${10}\n+# PhyloNet install dir\n+phylonet_install_dir=${11}\n+# Jane 4 install dir\n+jane_install_dir=${12}\n+# T-REX install dir\n+trex_install_dir=${13}\n+# Verbose string 'true' or 'false'\n+verbose=${14}\n+# Initial command that precedes call to software\n+# (example choosing virtualenv to workon)\n+init_command=${15}\n+# DIAMOND NR\n+diamond_nr=${16}\n+# Number threads\n+threads=${17}\n+\n+if [ \"$verbose\" == \"true\" ]\n+then\n+    echo \"working dir: $working_dir\"\n+    echo \"scripts_dir: $scripts_dir\"\n+    echo \"species tree: $species_tree_fp\"\n+    echo \"species genome: $species_genome_fp\"\n+    echo \"HMM model: $species_model_fp\"\n+    echo \"query genomes: $query_species_coding_seqs_fp\"\n+    echo \"species proteome: $ref_species_coding_seqs_fp\"\n+    echo \"gene trees: $gene_tree_dir\"\n+    echo \"gene MSAs: $gene_msa_dir\"\n+    echo \"blast nr: ${blast_nr}\"\n+    echo \"PhyloNet install dir: $phylonet_install_dir\"\n+    echo \"Jane 4 install dir: $jane_install_dir\"\n+    echo \"T-REX install dir: $trex_install_dir\"\n+fi\n+\n+mkdir -p \"${working_dir}/diamond\"\n+filename=$(basename \"${query_species_coding_seqs_fp}\")\n+diamond_output=${working_dir}/diamond/$filename\n+## launch DIAMOND if alignments don't exist for genome","path":"benchmark/launch_benchmark.sh","position":71,"original_position":71,"commit_id":"49281e1cc9254be30faa501de7134b4cd8d59aaa","original_commit_id":"49281e1cc9254be30faa501de7134b4cd8d59aaa","user":{"login":"ekopylova","id":6933444,"avatar_url":"https://avatars.githubusercontent.com/u/6933444?v=3","gravatar_id":"","url":"https://api.github.com/users/ekopylova","html_url":"https://github.com/ekopylova","followers_url":"https://api.github.com/users/ekopylova/followers","following_url":"https://api.github.com/users/ekopylova/following{/other_user}","gists_url":"https://api.github.com/users/ekopylova/gists{/gist_id}","starred_url":"https://api.github.com/users/ekopylova/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/ekopylova/subscriptions","organizations_url":"https://api.github.com/users/ekopylova/orgs","repos_url":"https://api.github.com/users/ekopylova/repos","events_url":"https://api.github.com/users/ekopylova/events{/privacy}","received_events_url":"https://api.github.com/users/ekopylova/received_events","type":"User","site_admin":false},"body":"No, it's needed, forgot to uncomment ..","created_at":"2016-01-15T15:45:59Z","updated_at":"2016-01-15T15:45:59Z","html_url":"https://github.com/biocore/WGS-HGT/pull/18#discussion_r49867480","pull_request_url":"https://api.github.com/repos/biocore/WGS-HGT/pulls/18","_links":{"self":{"href":"https://api.github.com/repos/biocore/WGS-HGT/pulls/comments/49867480"},"html":{"href":"https://github.com/biocore/WGS-HGT/pull/18#discussion_r49867480"},"pull_request":{"href":"https://api.github.com/repos/biocore/WGS-HGT/pulls/18"}}},"pull_request":{"url":"https://api.github.com/repos/biocore/WGS-HGT/pulls/18","id":56049928,"html_url":"https://github.com/biocore/WGS-HGT/pull/18","diff_url":"https://github.com/biocore/WGS-HGT/pull/18.diff","patch_url":"https://github.com/biocore/WGS-HGT/pull/18.patch","issue_url":"https://api.github.com/repos/biocore/WGS-HGT/issues/18","number":18,"state":"open","locked":false,"title":"Update benchmark layout, add main launch script","user":{"login":"ekopylova","id":6933444,"avatar_url":"https://avatars.githubusercontent.com/u/6933444?v=3","gravatar_id":"","url":"https://api.github.com/users/ekopylova","html_url":"https://github.com/ekopylova","followers_url":"https://api.github.com/users/ekopylova/followers","following_url":"https://api.github.com/users/ekopylova/following{/other_user}","gists_url":"https://api.github.com/users/ekopylova/gists{/gist_id}","starred_url":"https://api.github.com/users/ekopylova/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/ekopylova/subscriptions","organizations_url":"https://api.github.com/users/ekopylova/orgs","repos_url":"https://api.github.com/users/ekopylova/repos","events_url":"https://api.github.com/users/ekopylova/events{/privacy}","received_events_url":"https://api.github.com/users/ekopylova/received_events","type":"User","site_admin":false},"body":"1. Update benchmark to call individual scripts for launching software (rather than all in one call)\r\n2. Add launch_benchmark.sh which contains code to build databases (DIAMOND), HMM models (GeneMarkS), determine orthologous gene families, MSAs and trees, and then passes all of this information to launch_software.sh\r\n3. Use scikit-bio development version that supports TabularMSA and soon GenBank parsing","created_at":"2016-01-14T15:32:36Z","updated_at":"2016-01-15T15:45:59Z","closed_at":null,"merged_at":null,"merge_commit_sha":"e799d2c1fe4db59de8d24dc92be89482d8532dc5","assignee":null,"milestone":null,"commits_url":"https://api.github.com/repos/biocore/WGS-HGT/pulls/18/commits","review_comments_url":"https://api.github.com/repos/biocore/WGS-HGT/pulls/18/comments","review_comment_url":"https://api.github.com/repos/biocore/WGS-HGT/pulls/comments{/number}","comments_url":"https://api.github.com/repos/biocore/WGS-HGT/issues/18/comments","statuses_url":"https://api.github.com/repos/biocore/WGS-HGT/statuses/49281e1cc9254be30faa501de7134b4cd8d59aaa","head":{"label":"ekopylova:add_tools","ref":"add_tools","sha":"49281e1cc9254be30faa501de7134b4cd8d59aaa","user":{"login":"ekopylova","id":6933444,"avatar_url":"https://avatars.githubusercontent.com/u/6933444?v=3","gravatar_id":"","url":"https://api.github.com/users/ekopylova","html_url":"https://github.com/ekopylova","followers_url":"https://api.github.com/users/ekopylova/followers","following_url":"https://api.github.com/users/ekopylova/following{/other_user}","gists_url":"https://api.github.com/users/ekopylova/gists{/gist_id}","starred_url":"https://api.github.com/users/ekopylova/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/ekopylova/subscriptions","organizations_url":"https://api.github.com/users/ekopylova/orgs","repos_url":"https://api.github.com/users/ekopylova/repos","events_url":"https://api.github.com/users/ekopylova/events{/privacy}","received_events_url":"https://api.github.com/users/ekopylova/received_events","type":"User","site_admin":false},"repo":{"id":42261137,"name":"WGS-HGT","full_name":"ekopylova/WGS-HGT","owner":{"login":"ekopylova","id":6933444,"avatar_url":"https://avatars.githubusercontent.com/u/6933444?v=3","gravatar_id":"","url":"https://api.github.com/users/ekopylova","html_url":"https://github.com/ekopylova","followers_url":"https://api.github.com/users/ekopylova/followers","following_url":"https://api.github.com/users/ekopylova/following{/other_user}","gists_url":"https://api.github.com/users/ekopylova/gists{/gist_id}","starred_url":"https://api.github.com/users/ekopylova/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/ekopylova/subscriptions","organizations_url":"https://api.github.com/users/ekopylova/orgs","repos_url":"https://api.github.com/users/ekopylova/repos","events_url":"https://api.github.com/users/ekopylova/events{/privacy}","received_events_url":"https://api.github.com/users/ekopylova/received_events","type":"User","site_admin":false},"private":false,"html_url":"https://github.com/ekopylova/WGS-HGT","description":"Workflow for detecting genome-wide horizontal gene transfers","fork":true,"url":"https://api.github.com/repos/ekopylova/WGS-HGT","forks_url":"https://api.github.com/repos/ekopylova/WGS-HGT/forks","keys_url":"https://api.github.com/repos/ekopylova/WGS-HGT/keys{/key_id}","collaborators_url":"https://api.github.com/repos/ekopylova/WGS-HGT/collaborators{/collaborator}","teams_url":"https://api.github.com/repos/ekopylova/WGS-HGT/teams","hooks_url":"https://api.github.com/repos/ekopylova/WGS-HGT/hooks","issue_events_url":"https://api.github.com/repos/ekopylova/WGS-HGT/issues/events{/number}","events_url":"https://api.github.com/repos/ekopylova/WGS-HGT/events","assignees_url":"https://api.github.com/repos/ekopylova/WGS-HGT/assignees{/user}","branches_url":"https://api.github.com/repos/ekopylova/WGS-HGT/branches{/branch}","tags_url":"https://api.github.com/repos/ekopylova/WGS-HGT/tags","blobs_url":"https://api.github.com/repos/ekopylova/WGS-HGT/git/blobs{/sha}","git_tags_url":"https://api.github.com/repos/ekopylova/WGS-HGT/git/tags{/sha}","git_refs_url":"https://api.github.com/repos/ekopylova/WGS-HGT/git/refs{/sha}","trees_url":"https://api.github.com/repos/ekopylova/WGS-HGT/git/trees{/sha}","statuses_url":"https://api.github.com/repos/ekopylova/WGS-HGT/statuses/{sha}","languages_url":"https://api.github.com/repos/ekopylova/WGS-HGT/languages","stargazers_url":"https://api.github.com/repos/ekopylova/WGS-HGT/stargazers","contributors_url":"https://api.github.com/repos/ekopylova/WGS-HGT/contributors","subscribers_url":"https://api.github.com/repos/ekopylova/WGS-HGT/subscribers","subscription_url":"https://api.github.com/repos/ekopylova/WGS-HGT/subscription","commits_url":"https://api.github.com/repos/ekopylova/WGS-HGT/commits{/sha}","git_commits_url":"https://api.github.com/repos/ekopylova/WGS-HGT/git/commits{/sha}","comments_url":"https://api.github.com/repos/ekopylova/WGS-HGT/comments{/number}","issue_comment_url":"https://api.github.com/repos/ekopylova/WGS-HGT/issues/comments{/number}","contents_url":"https://api.github.com/repos/ekopylova/WGS-HGT/contents/{+path}","compare_url":"https://api.github.com/repos/ekopylova/WGS-HGT/compare/{base}...{head}","merges_url":"https://api.github.com/repos/ekopylova/WGS-HGT/merges","archive_url":"https://api.github.com/repos/ekopylova/WGS-HGT/{archive_format}{/ref}","downloads_url":"https://api.github.com/repos/ekopylova/WGS-HGT/downloads","issues_url":"https://api.github.com/repos/ekopylova/WGS-HGT/issues{/number}","pulls_url":"https://api.github.com/repos/ekopylova/WGS-HGT/pulls{/number}","milestones_url":"https://api.github.com/repos/ekopylova/WGS-HGT/milestones{/number}","notifications_url":"https://api.github.com/repos/ekopylova/WGS-HGT/notifications{?since,all,participating}","labels_url":"https://api.github.com/repos/ekopylova/WGS-HGT/labels{/name}","releases_url":"https://api.github.com/repos/ekopylova/WGS-HGT/releases{/id}","created_at":"2015-09-10T17:55:21Z","updated_at":"2016-01-11T16:28:02Z","pushed_at":"2016-01-14T16:06:30Z","git_url":"git://github.com/ekopylova/WGS-HGT.git","ssh_url":"git@github.com:ekopylova/WGS-HGT.git","clone_url":"https://github.com/ekopylova/WGS-HGT.git","svn_url":"https://github.com/ekopylova/WGS-HGT","homepage":null,"size":110,"stargazers_count":0,"watchers_count":0,"language":"Python","has_issues":false,"has_downloads":true,"has_wiki":true,"has_pages":false,"forks_count":0,"mirror_url":null,"open_issues_count":0,"forks":0,"open_issues":0,"watchers":0,"default_branch":"master"}},"base":{"label":"biocore:master","ref":"master","sha":"3f676dafd951fcd747ea9fee7733bd333014cd41","user":{"login":"biocore","id":6241857,"avatar_url":"https://avatars.githubusercontent.com/u/6241857?v=3","gravatar_id":"","url":"https://api.github.com/users/biocore","html_url":"https://github.com/biocore","followers_url":"https://api.github.com/users/biocore/followers","following_url":"https://api.github.com/users/biocore/following{/other_user}","gists_url":"https://api.github.com/users/biocore/gists{/gist_id}","starred_url":"https://api.github.com/users/biocore/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/biocore/subscriptions","organizations_url":"https://api.github.com/users/biocore/orgs","repos_url":"https://api.github.com/users/biocore/repos","events_url":"https://api.github.com/users/biocore/events{/privacy}","received_events_url":"https://api.github.com/users/biocore/received_events","type":"Organization","site_admin":false},"repo":{"id":41323398,"name":"WGS-HGT","full_name":"biocore/WGS-HGT","owner":{"login":"biocore","id":6241857,"avatar_url":"https://avatars.githubusercontent.com/u/6241857?v=3","gravatar_id":"","url":"https://api.github.com/users/biocore","html_url":"https://github.com/biocore","followers_url":"https://api.github.com/users/biocore/followers","following_url":"https://api.github.com/users/biocore/following{/other_user}","gists_url":"https://api.github.com/users/biocore/gists{/gist_id}","starred_url":"https://api.github.com/users/biocore/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/biocore/subscriptions","organizations_url":"https://api.github.com/users/biocore/orgs","repos_url":"https://api.github.com/users/biocore/repos","events_url":"https://api.github.com/users/biocore/events{/privacy}","received_events_url":"https://api.github.com/users/biocore/received_events","type":"Organization","site_admin":false},"private":false,"html_url":"https://github.com/biocore/WGS-HGT","description":"Workflow for detecting genome-wide horizontal gene transfers","fork":false,"url":"https://api.github.com/repos/biocore/WGS-HGT","forks_url":"https://api.github.com/repos/biocore/WGS-HGT/forks","keys_url":"https://api.github.com/repos/biocore/WGS-HGT/keys{/key_id}","collaborators_url":"https://api.github.com/repos/biocore/WGS-HGT/collaborators{/collaborator}","teams_url":"https://api.github.com/repos/biocore/WGS-HGT/teams","hooks_url":"https://api.github.com/repos/biocore/WGS-HGT/hooks","issue_events_url":"https://api.github.com/repos/biocore/WGS-HGT/issues/events{/number}","events_url":"https://api.github.com/repos/biocore/WGS-HGT/events","assignees_url":"https://api.github.com/repos/biocore/WGS-HGT/assignees{/user}","branches_url":"https://api.github.com/repos/biocore/WGS-HGT/branches{/branch}","tags_url":"https://api.github.com/repos/biocore/WGS-HGT/tags","blobs_url":"https://api.github.com/repos/biocore/WGS-HGT/git/blobs{/sha}","git_tags_url":"https://api.github.com/repos/biocore/WGS-HGT/git/tags{/sha}","git_refs_url":"https://api.github.com/repos/biocore/WGS-HGT/git/refs{/sha}","trees_url":"https://api.github.com/repos/biocore/WGS-HGT/git/trees{/sha}","statuses_url":"https://api.github.com/repos/biocore/WGS-HGT/statuses/{sha}","languages_url":"https://api.github.com/repos/biocore/WGS-HGT/languages","stargazers_url":"https://api.github.com/repos/biocore/WGS-HGT/stargazers","contributors_url":"https://api.github.com/repos/biocore/WGS-HGT/contributors","subscribers_url":"https://api.github.com/repos/biocore/WGS-HGT/subscribers","subscription_url":"https://api.github.com/repos/biocore/WGS-HGT/subscription","commits_url":"https://api.github.com/repos/biocore/WGS-HGT/commits{/sha}","git_commits_url":"https://api.github.com/repos/biocore/WGS-HGT/git/commits{/sha}","comments_url":"https://api.github.com/repos/biocore/WGS-HGT/comments{/number}","issue_comment_url":"https://api.github.com/repos/biocore/WGS-HGT/issues/comments{/number}","contents_url":"https://api.github.com/repos/biocore/WGS-HGT/contents/{+path}","compare_url":"https://api.github.com/repos/biocore/WGS-HGT/compare/{base}...{head}","merges_url":"https://api.github.com/repos/biocore/WGS-HGT/merges","archive_url":"https://api.github.com/repos/biocore/WGS-HGT/{archive_format}{/ref}","downloads_url":"https://api.github.com/repos/biocore/WGS-HGT/downloads","issues_url":"https://api.github.com/repos/biocore/WGS-HGT/issues{/number}","pulls_url":"https://api.github.com/repos/biocore/WGS-HGT/pulls{/number}","milestones_url":"https://api.github.com/repos/biocore/WGS-HGT/milestones{/number}","notifications_url":"https://api.github.com/repos/biocore/WGS-HGT/notifications{?since,all,participating}","labels_url":"https://api.github.com/repos/biocore/WGS-HGT/labels{/name}","releases_url":"https://api.github.com/repos/biocore/WGS-HGT/releases{/id}","created_at":"2015-08-24T19:43:04Z","updated_at":"2015-12-09T00:15:57Z","pushed_at":"2016-01-14T16:06:30Z","git_url":"git://github.com/biocore/WGS-HGT.git","ssh_url":"git@github.com:biocore/WGS-HGT.git","clone_url":"https://github.com/biocore/WGS-HGT.git","svn_url":"https://github.com/biocore/WGS-HGT","homepage":null,"size":317,"stargazers_count":1,"watchers_count":1,"language":"Python","has_issues":true,"has_downloads":true,"has_wiki":true,"has_pages":false,"forks_count":2,"mirror_url":null,"open_issues_count":9,"forks":2,"open_issues":9,"watchers":1,"default_branch":"master"}},"_links":{"self":{"href":"https://api.github.com/repos/biocore/WGS-HGT/pulls/18"},"html":{"href":"https://github.com/biocore/WGS-HGT/pull/18"},"issue":{"href":"https://api.github.com/repos/biocore/WGS-HGT/issues/18"},"comments":{"href":"https://api.github.com/repos/biocore/WGS-HGT/issues/18/comments"},"review_comments":{"href":"https://api.github.com/repos/biocore/WGS-HGT/pulls/18/comments"},"review_comment":{"href":"https://api.github.com/repos/biocore/WGS-HGT/pulls/comments{/number}"},"commits":{"href":"https://api.github.com/repos/biocore/WGS-HGT/pulls/18/commits"},"statuses":{"href":"https://api.github.com/repos/biocore/WGS-HGT/statuses/49281e1cc9254be30faa501de7134b4cd8d59aaa"}}}}