Andreas Tille pushed to branch master at Debian Med / graphbin
Commits: 715b4c14 by Andreas Tille at 2020-07-16T22:08:40+02:00 Slight polishing of manpage - - - - - b6da3fee by Andreas Tille at 2020-07-16T22:09:28+02:00 Some files are copyrighted 2020 - - - - - e9b24859 by Andreas Tille at 2020-07-16T22:10:12+02:00 BibTeX syntax for authors - - - - - fd2d958f by Andreas Tille at 2020-07-16T22:11:35+02:00 Add PMID - - - - - 6d3643f7 by Andreas Tille at 2020-07-16T22:40:17+02:00 DEP3 - - - - - 46063994 by Andreas Tille at 2020-07-16T22:54:25+02:00 Enable users to run autopkgtest script on local machine to on one hand allow to test the local installation and on the other hand have a working example at hand - - - - - 5d4caccc by Andreas Tille at 2020-07-16T22:55:40+02:00 Upload to new - - - - - 10 changed files: - + debian/README.test - debian/changelog - debian/copyright - + debian/graphbin-examples.docs - debian/graphbin-examples.install - + debian/graphbin.docs - debian/mans/graphbin.1 - debian/patches/fix_python_files.patch - debian/tests/run-unit-test - debian/upstream/metadata Changes: ===================================== debian/README.test ===================================== @@ -0,0 +1,9 @@ +Notes on how this package can be tested. +──────────────────────────────────────── + +This package can be tested by running the provided test: + + sudo apt install graphbin-examples + sh run-unit-test + +in order to confirm its integrity. ===================================== debian/changelog ===================================== @@ -1,4 +1,4 @@ -graphbin (1.1-1) UNRELEASED; urgency=medium +graphbin (1.1-1) unstable; urgency=medium * Initial release (Closes: #965079) ===================================== debian/copyright ===================================== @@ -3,7 +3,7 @@ Upstream-Name: graphbin Source: https://github.com/Vini2/GraphBin/ Files: * -Copyright: 2019 Graphbin Project +Copyright: 2019-2020 Graphbin Project License: GPL-2.0+ Files: debian/* ===================================== debian/graphbin-examples.docs ===================================== @@ -0,0 +1 @@ +debian/tests/run-unit-test ===================================== debian/graphbin-examples.install ===================================== @@ -1 +1 @@ -test_data/ usr/share/doc/graphbin-examples/ +test_data/* usr/share/doc/graphbin/examples/ ===================================== debian/graphbin.docs ===================================== @@ -0,0 +1 @@ +debian/README.test ===================================== debian/mans/graphbin.1 ===================================== @@ -2,7 +2,8 @@ .SH NAME graphbin \- refined binning of metagenomic contigs using assembly graphs .SH SYNOPSIS -usage: graphbin [\fI\,-h\/\fR] \fB\-\-assembler\fR \fI\,ASSEMBLER\/\fR \fB\-\-graph\fR \fI\,GRAPH\/\fR [\-\-paths \fI\,PATHS\/\fR] +.B graphbin +[\fI\,-h\/\fR] \fB\-\-assembler\fR \fI\,ASSEMBLER\/\fR \fB\-\-graph\fR \fI\,GRAPH\/\fR [\-\-paths \fI\,PATHS\/\fR] \fB\-\-binned\fR \fI\,BINNED\/\fR \fB\-\-output\fR \fI\,OUTPUT\/\fR [\-\-prefix \fI\,PREFIX\/\fR] [\-\-max_iteration \fI\,MAX_ITERATION\/\fR] [\-\-diff_threshold\fI\, DIFF_THRESHOLD\/\fR] @@ -13,6 +14,7 @@ the contig connectivity information from the assembly graph to bin contigs. It utilizes the binning result of an existing binning tool and a label propagation algorithm to correct mis\-binned contigs and predict the labels of contigs which are discarded due to short length. +.SH OPTIONS .SS "optional arguments:" .TP \fB\-h\fR, \fB\-\-help\fR ===================================== debian/patches/fix_python_files.patch ===================================== @@ -1,3 +1,7 @@ +Author: Shayan Doust +Last-Update: 2020-07-15 18:51:16 +0100 +Description: Add missing subprocess import + --- graphbin.orig/support/prepResult.py +++ graphbin/support/prepResult.py @@ -13,6 +13,7 @@ @@ -8,10 +12,3 @@ from Bio import SeqIO -@@ -209,4 +210,4 @@ - # Exit program - #-------------- - --print("\nThank you for using prepResult for GraphBin!\n") -\ No newline at end of file -+print("\nThank you for using prepResult for GraphBin!\n") ===================================== debian/tests/run-unit-test ===================================== @@ -1,22 +1,23 @@ #!/bin/bash set -e +pkg=graphbin + export LC_ALL=C.UTF-8 if [ "${AUTOPKGTEST_TMP}" = "" ] ; then AUTOPKGTEST_TMP=$(mktemp -d /tmp/${pkg}-test.XXXXXX) - # Double quote below to expand the temporary directory variable now versus - # later is on purpose. - # shellcheck disable=SC2064 trap "rm -rf ${AUTOPKGTEST_TMP}" 0 INT QUIT ABRT PIPE TERM fi BINNED_RESULTS="results/graphbin_output.csv" UNBINNED_CONTIGS="results/graphbin_unbinned.csv" -cp -a test_data/ "${AUTOPKGTEST_TMP}" +cp -a /usr/share/doc/${pkg}/examples/* "${AUTOPKGTEST_TMP}" +cd "${AUTOPKGTEST_TMP}" +gunzip -r * # Test graphbin with megahit assembler -cd "${AUTOPKGTEST_TMP}"/test_data/ESC_MEGAHIT/ +cd "${AUTOPKGTEST_TMP}"/ESC_MEGAHIT/ graphbin --assembler megahit --graph final.gfa --binned maxbin_contig_bins.csv --output results/ # Run basic check to see if output and unbinned files exist and are of non-zero byte size @@ -29,7 +30,7 @@ else fi # Test graphbin with sga assembler -cd "${AUTOPKGTEST_TMP}"/test_data/ESC_SGA/ +cd "${AUTOPKGTEST_TMP}"/ESC_SGA/ graphbin --assembler sga --graph default-graph.asqg --binned maxbin_contig_bins.csv --output results/ if [ -s "$BINNED_RESULTS" ] && [ -s "$UNBINNED_CONTIGS" ] @@ -41,7 +42,7 @@ else fi # Test graphbin with spades assembler -cd "${AUTOPKGTEST_TMP}"/test_data/ESC_metaSPAdes/ +cd "${AUTOPKGTEST_TMP}"/ESC_metaSPAdes/ graphbin --assembler spades --graph assembly_graph_with_scaffolds.gfa --paths contigs.paths --binned maxbin_contig_bins.csv --output results/ if [ -s "$BINNED_RESULTS" ] && [ -s "$UNBINNED_CONTIGS" ] ===================================== debian/upstream/metadata ===================================== @@ -1,13 +1,14 @@ Bug-Database: https://github.com/Vini2/GraphBin/issues Bug-Submit: https://github.com/Vini2/GraphBin/issues/new Reference: - Author: Vijini Mallawaarachchi, Anuradha Wickramarachchi & Yu Lin + Author: Vijini Mallawaarachchi and Anuradha Wickramarachchi and Yu Lin Title: "GraphBin: refined binning of metagenomic contigs using assembly graphs" Journal: Bioinformatics Year: 2020 Volume: 36 Pages: 3307-3313 DOI: 10.1093/bioinformatics/btaa180 + PMID: 32167528 URL: https://doi.org/10.1093/bioinformatics/btaa180 Repository: https://github.com/Vini2/GraphBin.git Repository-Browse: https://github.com/Vini2/GraphBin View it on GitLab: https://salsa.debian.org/med-team/graphbin/-/compare/4677b0cef6a2e8be9ee752bf85da7b6e96e70b61...5d4caccc73fec5b12b53f040ba523f4bc2ae9f60 -- View it on GitLab: https://salsa.debian.org/med-team/graphbin/-/compare/4677b0cef6a2e8be9ee752bf85da7b6e96e70b61...5d4caccc73fec5b12b53f040ba523f4bc2ae9f60 You're receiving this email because of your account on salsa.debian.org.
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