[med-svn] [Git][med-team/vt][master] 4 commits: Add publication and Conda id

Andreas Tille gitlab at salsa.debian.org
Thu Jun 18 11:27:16 BST 2020 


Andreas Tille pushed to branch master at Debian Med / vt


Commits:
65dbddcf by Andreas Tille at 2020-06-18T11:29:50+02:00
Add publication and Conda id

- - - - -
077a8a07 by Andreas Tille at 2020-06-18T11:34:15+02:00
Enhance long description from publication abstract giving more relevant for users than technical details what was used for linking

- - - - -
8dd227ca by Andreas Tille at 2020-06-18T11:52:23+02:00
Add more verbose test using example data

- - - - -
f73a6884 by Andreas Tille at 2020-06-18T11:59:28+02:00
Add simple manpage

- - - - -


11 changed files:

- + debian/README.test
- debian/control
- + debian/createmanpages
- + debian/manpages
- debian/tests/control
- + debian/tests/run-unit-test
- + debian/upstream/metadata
- + debian/vt-examples.install
- + debian/vt.1
- + debian/vt.docs
- debian/install → debian/vt.install


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:
+
+    apt install vt-examples
+    sh run-unit-test
+
+in order to confirm its integrity.


=====================================
debian/control
=====================================
@@ -27,10 +27,26 @@ Architecture: any
 Depends: ${shlibs:Depends},
          ${misc:Depends},
          r-base-core,
-Description: Tool set for short variant discovery in genetic sequence data
+Description: toolset for short variant discovery in genetic sequence data
  vt is a variant tool set that discovers short variants from Next Generation
  Sequencing data.
  .
- Visit http://genome.sph.umich.edu/wiki/vt for instructions.
+ Vt-normalize is a tool to normalize representation of genetic variants in
+ the VCF.  Variant normalization is formally defined as the consistent
+ representation of genetic variants in an unambiguous and concise way.  In
+ vt a simple general algorithm to enforce this is implemented.
+
+Package: vt-examples
+Architecture: all
+Depends: ${misc:Depends},
+Enhances: vt
+Description: toolset for short variant discovery in genetic sequence data (examples)
+ vt is a variant tool set that discovers short variants from Next Generation
+ Sequencing data.
+ .
+ Vt-normalize is a tool to normalize representation of genetic variants in
+ the VCF.  Variant normalization is formally defined as the consistent
+ representation of genetic variants in an unambiguous and concise way.  In
+ vt a simple general algorithm to enforce this is implemented.
  .
- vt uses htslib, tclap, Rmath, pcre2 and libsvm.
+ This package contains some example data.


=====================================
debian/createmanpages
=====================================
@@ -0,0 +1,28 @@
+#!/bin/sh
+MANDIR=debian
+mkdir -p $MANDIR
+
+VERSION=`dpkg-parsechangelog | awk '/^Version:/ {print $2}' | sed -e 's/^[0-9]*://' -e 's/-.*//' -e 's/[+~]dfsg$//'`
+NAME=`grep "^Description:" debian/control | sed 's/^Description: *//' | head -n1`
+PROGNAME=`grep "^Package:" debian/control | sed 's/^Package: *//' | head -n1`
+
+AUTHOR=".SH AUTHOR\n \
+This manpage was written by $DEBFULLNAME for the Debian distribution and\n \
+can be used for any other usage of the program.\
+"
+
+# If program name is different from package name or title should be
+# different from package short description change this here
+progname=${PROGNAME}
+help2man --no-info --no-discard-stderr --help-option=" " \
+         --name="$NAME" \
+            --version-string="$VERSION" ${progname} > $MANDIR/${progname}.1
+echo $AUTHOR >> $MANDIR/${progname}.1
+
+echo "$MANDIR/*.1" > debian/manpages
+
+cat <<EOT
+Please enhance the help2man output.
+The following web page might be helpful in doing so:
+    http://liw.fi/manpages/
+EOT


=====================================
debian/manpages
=====================================
@@ -0,0 +1 @@
+debian/*.1


=====================================
debian/tests/control
=====================================
@@ -1,2 +1,3 @@
-Tests: basic
-Depends: vt
+Tests: basic, run-unit-test
+Depends: @
+Restrictions: allow-stderr


=====================================
debian/tests/run-unit-test
=====================================
@@ -0,0 +1,19 @@
+#!/bin/bash
+set -e
+
+pkg=vt
+
+export LC_ALL=C.UTF-8
+if [ "${AUTOPKGTEST_TMP}" = "" ] ; then
+  AUTOPKGTEST_TMP=$(mktemp -d /tmp/${pkg}-test.XXXXXX)
+  trap "rm -rf ${AUTOPKGTEST_TMP}" 0 INT QUIT ABRT PIPE TERM
+fi
+
+cp -a /usr/share/doc/${pkg}/examples/* "${AUTOPKGTEST_TMP}"
+
+cd "${AUTOPKGTEST_TMP}"
+
+find . \( -name "*.vcf.gz" -o -name "*.gzi.gz" -o -name "*.sh.gz" \) -exec gunzip \{\} \;
+
+sed -i 's:VT=${DIR}/../vt:VT=/usr/bin/vt:' test.sh
+bash ./test.sh


=====================================
debian/upstream/metadata
=====================================
@@ -0,0 +1,16 @@
+Reference:
+  Author: Adrian Tan and Gonçalo R. Abecasis and Hyun Min Kang
+  Title: Unified representation of genetic variants
+  Journal: Bioinformatics
+  Year: 2015
+  Volume: 31
+  Number: 13
+  Pages: 2202–2204
+  DOI: 10.1093/bioinformatics
+  PMID: 25701572
+  PMCID: PMC4481842
+  URL: https://academic.oup.com/bioinformatics/article/31/13/2202/196142
+  eprint: https://academic.oup.com/bioinformatics/article-pdf/31/13/2202/17122489/btv112.pdf
+Registry:
+  - Name: conda:bioconda
+    Entry: vt


=====================================
debian/vt-examples.install
=====================================
@@ -0,0 +1,2 @@
+test/*				usr/share/doc/vt/examples
+debian/tests/run-unit-test	usr/share/doc/vt


=====================================
debian/vt.1
=====================================
@@ -0,0 +1,73 @@
+.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.15.
+.TH VT "1" "June 2020" "vt 0.57721+ds" "User Commands"
+.SH NAME
+vt \- toolset for short variant discovery in genetic sequence data
+.SH SYNOPSIS
+.B vt
+<tool> [options]
+.SH TOOLS
+.TP
+view
+view vcf/vcf.gz/bcf files
+.TP
+index
+index vcf.gz/bcf files
+.TP
+normalize
+normalize variants
+.TP
+decompose
+decompose variants
+.TP
+uniq
+drop duplicate variants
+.TP
+cat
+concatenate VCF files
+.TP
+paste
+paste VCF files
+.TP
+sort
+sort VCF files
+.TP
+subset
+subset VCF file to variants polymorphic in a sample
+.TP
+peek
+summary of variants in the vcf file
+.TP
+partition
+partition variants
+.TP
+multi_partition
+partition variants from multiple VCF files
+.TP
+annotate_variants
+annotate variants
+.TP
+annotate_db_rsid
+annotate variants with dbSNP rsid
+.TP
+annotate_1000g
+annotate variants with 1000 Genomes variants
+.TP
+annotate_regions
+annotate regions
+.TP
+compute_concordance
+compute genotype concordance between 2 call sets
+.TP
+compute_features
+compute genotype likelihood based statistics
+.TP
+discover
+discover variants
+.TP
+genotype
+genotype variants
+.SH SEE ALSO
+Help page on http://statgen.sph.umich.edu/wiki/Vt
+.SH AUTHOR
+ This manpage was written by Andreas Tille for the Debian distribution and
+ can be used for any other usage of the program.


=====================================
debian/vt.docs
=====================================
@@ -0,0 +1 @@
+debian/README.test


=====================================
debian/install → debian/vt.install
=====================================



View it on GitLab: https://salsa.debian.org/med-team/vt/-/compare/8d7a6047a9b5ecb846da38a0175ec394758eef8c...f73a688485e3cbfcb87d4d13ddcdfd9c247aee4b

-- 
View it on GitLab: https://salsa.debian.org/med-team/vt/-/compare/8d7a6047a9b5ecb846da38a0175ec394758eef8c...f73a688485e3cbfcb87d4d13ddcdfd9c247aee4b
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