[med-svn] [Git][med-team/beagle][master] 3 commits: Update d/changelog
Dylan Aïssi
gitlab at salsa.debian.org
Mon Oct 14 20:48:23 BST 2019
Dylan Aïssi pushed to branch master at Debian Med / beagle
Commits:
1189b855 by Dylan Aïssi at 2019-10-14T19:33:06Z
Update d/changelog
- - - - -
8205bf03 by Dylan Aïssi at 2019-10-14T19:39:52Z
Update upstream docs
- - - - -
21a6e931 by Dylan Aïssi at 2019-10-14T19:47:43Z
Standards-Version: 4.4.1 (no changes needed)
- - - - -
6 changed files:
- debian/README.source
- debian/changelog
- debian/control
- debian/upstream.docs/README
- debian/upstream.docs/release_notes
- debian/upstream.docs/run.beagle.example
Changes:
=====================================
debian/README.source
=====================================
@@ -2,7 +2,7 @@ How to rename the upstream sources
=============================================
uscan
-mv beagle_180703+dfsg.orig.tar.xz \
- beagle_5.0-180703+dfsg.orig.tar.xz
+mv beagle_190921+dfsg.orig.tar.xz \
+ beagle_5.1-190921+dfsg.orig.tar.xz
-- Dylan Aïssi <bob.dybian at gmail.com> Tue, 30 Jan 2018 23:28:16 +0100
=====================================
debian/changelog
=====================================
@@ -1,3 +1,10 @@
+beagle (5.1-190921+dfsg-1) UNRELEASED; urgency=medium
+
+ * New upstream release.
+ * Standards-Version: 4.4.1 (no changes needed).
+
+ -- Dylan Aïssi <daissi at debian.org> Mon, 14 Oct 2019 21:31:05 +0200
+
beagle (5.1-190824+dfsg-2) unstable; urgency=medium
* Team upload.
=====================================
debian/control
=====================================
@@ -7,7 +7,7 @@ Build-Depends: debhelper-compat (= 12),
javahelper
Build-Depends-Indep: default-jdk,
libhtsjdk-java
-Standards-Version: 4.4.0
+Standards-Version: 4.4.1
Vcs-Browser: https://salsa.debian.org/med-team/beagle
Vcs-Git: https://salsa.debian.org/med-team/beagle.git
Homepage: https://faculty.washington.edu/browning/beagle/beagle.html
=====================================
debian/upstream.docs/README
=====================================
@@ -5,6 +5,6 @@
wget https://faculty.washington.edu/browning/beagle/beagle5_release_notes -O release_notes
wget https://faculty.washington.edu/browning/beagle/beagle_5.1_12Aug19.pdf -O beagle_5.1.pdf
- wget https://faculty.washington.edu/browning/beagle/run.beagle.24Aug19.3e8.example -O run.beagle.example
- wget https://faculty.washington.edu/browning/beagle/test.24Aug19.3e8.vcf.gz -O test.vcf.gz && \
+ wget https://faculty.washington.edu/browning/beagle/run.beagle.21Sep19.ec3.example -O run.beagle.example
+ wget https://faculty.washington.edu/browning/beagle/test.21Sep19.ec3.vcf.gz -O test.vcf.gz && \
gunzip test.vcf.gz
=====================================
debian/upstream.docs/release_notes
=====================================
@@ -73,3 +73,8 @@ Beagle 5.1 (13Aug19.a31) release notes
Beagle 5.1 (24Aug19.3e8) release notes
============================================
* Fixed a bug that can arise when phasing inbred samples
+
+Beagle 5.1 (21Sep19.ec3) release notes
+============================================
+* Fixed bugs when phasing or imputing using a reference panel
+
=====================================
debian/upstream.docs/run.beagle.example
=====================================
@@ -1,47 +1,47 @@
#!/bin/bash
-if [ ! -f beagle.24Aug19.3e8.jar ]; then
+if [ ! -f beagle.21Sep19.ec3.jar ]; then
echo
- echo "Downloading beagle.24Aug19.3e8.jar"
- wget http://faculty.washington.edu/browning/beagle/beagle.24Aug19.3e8.jar
+ echo "Downloading beagle.21Sep19.ec3.jar"
+ wget http://faculty.washington.edu/browning/beagle/beagle.21Sep19.ec3.jar
fi
-if [ ! -f bref3.24Aug19.3e8.jar ]; then
+if [ ! -f bref3.21Sep19.ec3.jar ]; then
echo
- echo "Downloading bref3.24Aug19.3e8.jar"
- wget http://faculty.washington.edu/browning/beagle/bref3.24Aug19.3e8.jar
+ echo "Downloading bref3.21Sep19.ec3.jar"
+ wget http://faculty.washington.edu/browning/beagle/bref3.21Sep19.ec3.jar
fi
echo
-if [ ! -f test.24Aug19.3e8.vcf.gz ]; then
+if [ ! -f test.21Sep19.ec3.vcf.gz ]; then
echo
- echo "*** Downloading some 1000 Genomes Project data to file: test.24Aug19.3e8.vcf.gz ***"
- wget http://faculty.washington.edu/browning/beagle/test.24Aug19.3e8.vcf.gz
+ echo "*** Downloading some 1000 Genomes Project data to file: test.21Sep19.ec3.vcf.gz ***"
+ wget http://faculty.washington.edu/browning/beagle/test.21Sep19.ec3.vcf.gz
fi
echo
-echo "*** Creating test files: ref.24Aug19.3e8.vcf.gz target.24Aug19.3e8.vcf.gz ***"
+echo "*** Creating test files: ref.21Sep19.ec3.vcf.gz target.21Sep19.ec3.vcf.gz ***"
echo
-zcat test.24Aug19.3e8.vcf.gz | cut -f1-190 | tr '/' '|' | gzip > ref.24Aug19.3e8.vcf.gz
-zcat test.24Aug19.3e8.vcf.gz | cut -f1-9,191-200 | gzip > target.24Aug19.3e8.vcf.gz
+zcat test.21Sep19.ec3.vcf.gz | cut -f1-190 | tr '/' '|' | gzip > ref.21Sep19.ec3.vcf.gz
+zcat test.21Sep19.ec3.vcf.gz | cut -f1-9,191-200 | gzip > target.21Sep19.ec3.vcf.gz
echo
echo "*** Running test analysis with \"gt=\" argument ***"
echo
-java -jar beagle.24Aug19.3e8.jar gt=test.24Aug19.3e8.vcf.gz out=out.gt
+java -jar beagle.21Sep19.ec3.jar gt=test.21Sep19.ec3.vcf.gz out=out.gt
echo
echo "*** Running test analysis with \"ref=\" and \"gt=\" arguments ***"
echo
-java -jar beagle.24Aug19.3e8.jar ref=ref.24Aug19.3e8.vcf.gz gt=target.24Aug19.3e8.vcf.gz out=out.ref
+java -jar beagle.21Sep19.ec3.jar ref=ref.21Sep19.ec3.vcf.gz gt=target.21Sep19.ec3.vcf.gz out=out.ref
echo
echo "*** Making \"bref3\" file ***"
echo
-java -jar bref3.24Aug19.3e8.jar ref.24Aug19.3e8.vcf.gz > ref.24Aug19.3e8.bref3
+java -jar bref3.21Sep19.ec3.jar ref.21Sep19.ec3.vcf.gz > ref.21Sep19.ec3.bref3
echo
echo "*** Running test analysis with \"bref3\" file ***"
echo
-java -jar beagle.24Aug19.3e8.jar ref=ref.24Aug19.3e8.bref3 gt=target.24Aug19.3e8.vcf.gz out=out.bref3
+java -jar beagle.21Sep19.ec3.jar ref=ref.21Sep19.ec3.bref3 gt=target.21Sep19.ec3.vcf.gz out=out.bref3
View it on GitLab: https://salsa.debian.org/med-team/beagle/compare/d8d6175f10bd2bfb2e409bec23680bc3318cb64e...21a6e93102e4a423dc99a92158b3fd452b1d3428
--
View it on GitLab: https://salsa.debian.org/med-team/beagle/compare/d8d6175f10bd2bfb2e409bec23680bc3318cb64e...21a6e93102e4a423dc99a92158b3fd452b1d3428
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