[med-svn] [Git][med-team/abyss][master] 10 commits: cleanups on the testing script
Michael R. Crusoe
gitlab at salsa.debian.org
Sun Feb 17 13:22:55 GMT 2019
Michael R. Crusoe pushed to branch master at Debian Med / abyss
Commits:
45c04e63 by Michael R. Crusoe at 2019-02-17T11:00:21Z
cleanups on the testing script
- - - - -
5931e80e by Michael R. Crusoe at 2019-02-17T11:02:20Z
upgrade openmpi-bin from a suggests to a dependency
- - - - -
f615944a by Michael R. Crusoe at 2019-02-17T11:30:09Z
appease dh_missing
- - - - -
94c0fb7c by Michael R. Crusoe at 2019-02-17T13:05:23Z
make manual pages for the last two binaries
- - - - -
7bd90c84 by Michael R. Crusoe at 2019-02-17T13:05:23Z
Fix "implicit declaration of function"s in dialign/museq.c
- - - - -
75213389 by Michael R. Crusoe at 2019-02-17T13:05:24Z
forward the relevant patches
- - - - -
2fcc5b0e by Michael R. Crusoe at 2019-02-17T13:05:24Z
fix some spelling typos
- - - - -
285787ba by Michael R. Crusoe at 2019-02-17T13:06:50Z
add myself as an uploader
- - - - -
e414e5f5 by Michael R. Crusoe at 2019-02-17T13:16:42Z
register flowchart PDFs with doc-base
- - - - -
e2ef3271 by Michael R. Crusoe at 2019-02-17T13:20:05Z
upload to unstable
- - - - -
16 changed files:
- debian/changelog
- debian/control
- + debian/doc-base
- debian/docs
- debian/manpages
- + debian/not-installed
- debian/patches/abyss-32-bit.patch
- debian/patches/big_endian.patch
- debian/patches/fix_bash_script.patch
- + debian/patches/fix_implicit-function-declaration
- debian/patches/hurd.patch
- debian/patches/series
- + debian/patches/spelling
- debian/patches/strict_alignment.patch
- debian/rules
- debian/tests/run-unit-test
Changes:
=====================================
debian/changelog
=====================================
@@ -1,3 +1,14 @@
+abyss (2.1.5-7) unstable; urgency=medium
+
+ * Add myself as an uploader.
+ * The package openmpi-bin is now a required dependency for the abyss
+ binary package. Many thanks to ci.debian.org for bringing this to light.
+ * Fix "implicit declaration of function"s in dialign/museq.c
+ * Fix some spelling typos
+ * Register the flowchart PDFs with doc-base
+
+ -- Michael R. Crusoe <michael.crusoe at gmail.com> Sun, 17 Feb 2019 05:19:54 -0800
+
abyss (2.1.5-6) unstable; urgency=high
* Team upload.
=====================================
debian/control
=====================================
@@ -1,6 +1,7 @@
Source: abyss
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
-Uploaders: Andreas Tille <tille at debian.org>
+Uploaders: Andreas Tille <tille at debian.org>,
+ Michael R. Crusoe <michael.crusoe at gmail.com>
Section: science
Priority: optional
Build-Depends: debhelper (>= 12~),
@@ -11,7 +12,8 @@ Build-Depends: debhelper (>= 12~),
libtext-multimarkdown-perl,
libgtest-dev,
libsqlite3-dev,
- pkg-config
+ pkg-config,
+ help2man
Standards-Version: 4.3.0
Vcs-Browser: https://salsa.debian.org/med-team/abyss
Vcs-Git: https://salsa.debian.org/med-team/abyss.git
@@ -24,8 +26,10 @@ Depends: make,
${misc:Depends},
${perl:Depends},
bsdmainutils,
- openmpi-common
-Suggests: openmpi-bin
+# For openmpi error messages:
+ openmpi-common,
+# for /usr/bin/orted and possibly other MPI components:
+ openmpi-bin
Description: de novo, parallel, sequence assembler for short reads
ABySS is a de novo, parallel, sequence assembler that is designed for
short reads. It may be used to assemble genome or transcriptome
=====================================
debian/doc-base
=====================================
@@ -0,0 +1,8 @@
+Document: abyss-flowcharts
+Title: ABySS flowcharts
+Author: Tbe ABySS authors
+Abstract: The ABySS assembly pipeline and its intermediate files
+Section: Science/Biology
+
+Format: pdf
+Files: /usr/share/doc/abyss/flowchart*.pdf.gz
=====================================
debian/docs
=====================================
@@ -1,6 +1,7 @@
-README.md
+debian/tmp/usr/share/doc/abyss/README.md
README.html
-doc/flowchart.pdf
+debian/tmp/usr/share/doc/abyss/flowchart*.pdf
+debian/tmp/usr/share/doc/abyss/CITATION*
debian/tests/run-unit-test
debian/tests/test-data
debian/README.test
=====================================
debian/manpages
=====================================
@@ -1 +1 @@
-doc/*.1
+debian/tmp/usr/share/man/man1/*.1
=====================================
debian/not-installed
=====================================
@@ -0,0 +1,5 @@
+usr/share/doc/abyss/LICENSE
+usr/share/doc/abyss/COPYRIGHT
+
+# not true, but done in another way
+usr/share/doc/abyss/ChangeLog
=====================================
debian/patches/abyss-32-bit.patch
=====================================
@@ -1,5 +1,6 @@
Author: Graham Inggs <graham at nerve.org.za>
Last-Update: Thu, 16 Jul 2015 10:44:56 +0200
+Forwarded: https://github.com/bcgsc/abyss/pull/278
Bug-Debian: http://bugs.debian.org/780409
Description: Fix FTBFS on 32-bit architectures
Version 1.5.2-1 of abyss FTBFS on 32-bit architectures (armhf, i386 and
=====================================
debian/patches/big_endian.patch
=====================================
@@ -1,6 +1,7 @@
Author: Daniel Knezevic <Daniel.Knezevic at imgtec.com>
Last-Update: Fri, 9 Dec 2016 15:27:02 UTC
Bug-Debian: https://bugs.debian.org/847574
+Forwarded: https://github.com/bcgsc/abyss/pull/279
Description: Fix FTBFS on mips and other big-endian architectures
--- a/Common/Kmer.cpp
=====================================
debian/patches/fix_bash_script.patch
=====================================
@@ -1,5 +1,6 @@
Author: Andreas Tille <tille at debian.org>
Last-Update: Thu, 16 Jul 2015 10:50:15 +0200
+Forwarded: https://github.com/bcgsc/abyss/pull/280
Description: Script uses bash syntax so request bash interpreter
--- a/DataBase/abyss-db-txt
=====================================
debian/patches/fix_implicit-function-declaration
=====================================
@@ -0,0 +1,24 @@
+From: Michael R. Crusoe <michael.crusoe at gmail.com>
+Subject: Fix "implicit declaration of function"s
+Forwarded: https://github.com/bcgsc/abyss/pull/277
+
+Issues discovered courtesy the Debian Build Log Scanner
+
+--- abyss.orig/dialign/museq.c
++++ abyss/dialign/museq.c
+@@ -38,6 +38,7 @@
+ //extern void calc_weight(struct diag* dg, struct scr_matrix* smatrix,
+ // struct prob_dist *pdist);
+ //extern struct diag_col *create_diag_col(int seq_amount);
++extern void free_diag(struct diag* dg);
+ extern void free_diag_col(struct diag_col* dcol);
+ extern struct diag_col *find_all_diags(struct scr_matrix *smatrix,
+ struct prob_dist *pdist,
+@@ -51,6 +52,7 @@
+ extern struct prob_dist* calc_score_dist(struct scr_matrix *smatrix, int mxdlen);
+
+ // alig.c
++extern void free_alignment(struct alignment *algn);
+ extern struct alignment* create_empty_alignment(struct seq_col *scol);
+ //extern char adapt_diag(struct alignment *algn, struct scr_matrix *smatrix, struct diag* dg);
+ extern int simple_aligner(struct seq_col *scol, struct diag_col *dcol,
=====================================
debian/patches/hurd.patch
=====================================
@@ -1,6 +1,7 @@
From: Samuel Thibault <sthibault at debian.org>
Date: Wed, 23 Jan 2019 09:45:27 +0100
Bug-Debian: https://bugs.debian.org/920240
+Forwarded: https://github.com/bcgsc/abyss/pull/281
Description: Fix build on hurd due to missing header file
--- a/Common/MemoryUtil.h
=====================================
debian/patches/series
=====================================
@@ -5,3 +5,5 @@ fix_bash_script.patch
big_endian.patch
strict_alignment.patch
hurd.patch
+fix_implicit-function-declaration
+spelling
=====================================
debian/patches/spelling
=====================================
@@ -0,0 +1,110 @@
+From: Michael R. Crusoe <michael.crusoe at gmail.com>
+Subject: Fix spelling
+Forwarded: https://github.com/bcgsc/abyss/pull/282
+
+Spelling typos found via the Debian lintian checks
+--- abyss.orig/Consensus/Consensus.cpp
++++ abyss/Consensus/Consensus.cpp
+@@ -453,7 +453,7 @@
+ } else if (opt::verbose > 0) {
+ cerr << "warning: Contig " << it->first
+ << " was not supported by a complete read "
+- "and was ommited.\n";
++ "and was omitted.\n";
+ }
+ }
+ }
+--- abyss.orig/dialign/parameters.c
++++ abyss/dialign/parameters.c
+@@ -300,7 +300,7 @@
+ printf(" -n\tmaximum number of consecutive positions for window containing\n \tlow scoring positions \n \t\t[DEFAULT PROTEIN: 4]\n\t\t[DEFAULT DNA: 4]\n");
+ printf(" -g\tglobal minimum fragment length for stop criterion \n \t\t[DEFAULT PROTEIN: 40] \n\t\t[DEFAULT DNA: 40]\n");
+ printf(" -m\tminimal allowed average score in frag window containing low \n \tscoring positions \n \t\t[DEFAULT PROTEIN: 4.0]\n\t\t[DEFAULT DNA: 0.25]\n");
+- printf(" -o\twether overlap weights are calculated or not [DEFAULT 0]\n");
++ printf(" -o\twhether overlap weights are calculated or not [DEFAULT 0]\n");
+ printf(" -f\tminimum fragment length [DEFAULT 1]\n");
+ printf(" -r\tthreshold weight to consider the fragment at all [DEFAULT 0.0]\n");
+ printf(" -u\t[DEFAULT 0]\n");
+--- abyss.orig/dialign/parameters.h
++++ abyss/dialign/parameters.h
+@@ -90,7 +90,7 @@
+ *
+ *****************************/
+
+- // wether overlap weights are calculated or not
++ // whether overlap weights are calculated or not
+ int DO_OVERLAP; // = 0;
+
+ // minimum diag length
+--- abyss.orig/SimpleGraph/SimpleGraph.cpp
++++ abyss/SimpleGraph/SimpleGraph.cpp
+@@ -806,7 +806,7 @@
+ << g_minNumPairsUsed << ".\n";
+ if (g_minNumPairs < g_minNumPairsUsed)
+ cout << "Consider increasing the number of pairs "
+- "threshold paramter, n, to " << g_minNumPairsUsed
++ "threshold parameter, n, to " << g_minNumPairsUsed
+ << ".\n";
+ }
+
+--- abyss.orig/DataLayer/abyss-tofastq.cc
++++ abyss/DataLayer/abyss-tofastq.cc
+@@ -34,8 +34,8 @@
+ "\n"
+ " --cat concatenate the records [default]\n"
+ " -i, --interleave interleave the records\n"
+-" --fastq ouput FASTQ format [default]\n"
+-" --fasta ouput FASTA format\n"
++" --fastq output FASTQ format [default]\n"
++" --fasta output FASTA format\n"
+ " --bx copy SAM BX tag to output FASTA comment\n"
+ " --chastity discard unchaste reads [default]\n"
+ " --no-chastity do not discard unchaste reads\n"
+--- abyss.orig/Konnector/konnector.cc
++++ abyss/Konnector/konnector.cc
+@@ -128,7 +128,7 @@
+ " use 'nolimit' for no limit [nolimit]\n"
+ "\n"
+ " Note: --max-branches was not effective for truncating expensive searches,\n"
+-" and has been superceded by the --max-cost option.\n"
++" and has been superseded by the --max-cost option.\n"
+ "\n"
+ "Report bugs to <" PACKAGE_BUGREPORT ">.\n";
+
+@@ -864,7 +864,7 @@
+
+ updateCounters(params, result);
+
+- /* ouput merged / unmerged reads */
++ /* output merged / unmerged reads */
+
+ if (result.pathResult == FOUND_PATH &&
+ !exceedsMismatchThresholds(params, result)) {
+--- abyss.orig/Sealer/sealer.cc
++++ abyss/Sealer/sealer.cc
+@@ -124,12 +124,12 @@
+ " -F, --max-frag=N max fragment size in base pairs\n"
+ "\n"
+ " Note 1: --max-branches was not effective for truncating expensive searches,\n"
+-" and has been superceded by the --max-cost option.\n"
++" and has been superseded by the --max-cost option.\n"
+ "\n"
+ " Note 2: --max-frag was formerly used to determine the maximum gap\n"
+ " size that abyss-sealer would attempt to close, according to the formula\n"
+ " max_gap_size = max_frag - 2 * flank_length, where flank_length is\n"
+-" determined by the -L option. --max-frag is superceded by the more\n"
++" determined by the -L option. --max-frag is superseded by the more\n"
+ " intuitive -G (--max-gap-length) option. The related option --min-frag\n"
+ " does not seem to have any practical use.\n"
+ "\n"
+--- abyss.orig/doc/abyss-pe.1
++++ abyss/doc/abyss-pe.1
+@@ -24,7 +24,7 @@
+ .TP
+ .B lib
+ a quoted list of whitespace-separated paired-end library names. Use
+-this varible when assembling data from multiple paired-end libraries.
++this variable when assembling data from multiple paired-end libraries.
+ For each library name in lib, the user must define a variable on
+ the command line with the same name, which indicates the read files for
+ that library. See \fBEXAMPLES\fR below for a concrete example of usage.
=====================================
debian/patches/strict_alignment.patch
=====================================
@@ -1,6 +1,7 @@
Author: David Matthew Mattli <dmm at mattli.us>
Last-Change: Fri, 2 Feb 2018 15:28:32 +0000 (by James Clarke <jrtc27 at debian.org>)
Bug-Debian: https://bugs.debian.org/889147
+Forwarded: https://github.com/bcgsc/abyss/pull/279
Description: Fix strict alignment violation on sparc64
--- a/Common/Kmer.cpp
=====================================
debian/rules
=====================================
@@ -19,6 +19,12 @@ override_dh_auto_build:
override_dh_auto_install:
dh_auto_install --destdir=debian/tmp
+ PATH=debian/tmp/usr/bin:$(PATH) help2man --no-info \
+ -n "Estimate distances between contigs using paired-end alignments." \
+ DistanceEst > debian/tmp/usr/share/man/man1/DistanceEst.1
+ PATH=debian/tmp/usr/bin:$(PATH) help2man --no-info \
+ -n "Fill the paired-end fields of SAM alignments" abyss-fixmate \
+ > debian/tmp/usr/share/man/man1/abyss-fixmate.1
override_dh_install:
dh_install
=====================================
debian/tests/run-unit-test
=====================================
@@ -2,20 +2,23 @@
pkg=abyss
-if [ "$ADTTMP" = "" ] ; then
- ADTTMP=$(mktemp -d /tmp/${pkg}-test.XXXXXX)
- trap "rm -rf $ADTTMP" 0 INT QUIT ABRT PIPE TERM
+if [ "${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
-cd $ADTTMP
+cd "${AUTOPKGTEST_TMP}"
cp -a /usr/share/doc/${pkg}/test-data/ .
-gunzip -r *
+gunzip -r ./*
abyss-pe k=25 name=test in='test-data/reads1.fastq test-data/reads2.fastq'
-echo Testing mpi compilation
-/usr/lib/abyss/ABYSS-P --help
-
-
-
+# It is okay if the echo comman can't respect "-n" and includes a newline
+# shellcheck disable=SC2039
+echo -n Testing mpi compilation: ...
+/usr/lib/abyss/ABYSS-P --help > /dev/null
+echo " success!"
View it on GitLab: https://salsa.debian.org/med-team/abyss/compare/2424f7740fa1df15b1046a818242ab64c92e0c5c...e2ef3271de0b5803cbc48ba0205ea66f228e87ba
--
View it on GitLab: https://salsa.debian.org/med-team/abyss/compare/2424f7740fa1df15b1046a818242ab64c92e0c5c...e2ef3271de0b5803cbc48ba0205ea66f228e87ba
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