[med-svn] [Git][med-team/graphbin][master] 7 commits: Slight polishing of manpage
Andreas Tille
gitlab at salsa.debian.org
Thu Jul 16 22:00:53 BST 2020
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
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fd2d958f by Andreas Tille at 2020-07-16T22:11:35+02:00
Add PMID
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6d3643f7 by Andreas Tille at 2020-07-16T22:40:17+02:00
DEP3
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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
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