Dylan Aïssi pushed to branch master at Debian Med / beagle
Commits: 82bfe2ec by Dylan Aïssi at 2019-07-04T06:02:31Z Standards-Version: 4.3.0 (no changes needed) - - - - - 5adf6940 by Dylan Aïssi at 2019-07-04T06:10:49Z Update upstream docs - - - - - 5 changed files: - debian/changelog - debian/control - debian/upstream.docs/README - debian/upstream.docs/beagle_5.0.pdf - debian/upstream.docs/run.beagle.example Changes: ===================================== debian/changelog ===================================== @@ -1,6 +1,7 @@ beagle (5.0-190703+dfsg-1) UNRELEASED; urgency=medium * New upstream release. + * Standards-Version: 4.3.0 (no changes needed). -- Dylan Aïssi <[email protected]> Thu, 04 Jul 2019 07:49:33 +0200 ===================================== debian/control ===================================== @@ -7,7 +7,7 @@ Build-Depends: debhelper (>= 11~), javahelper Build-Depends-Indep: default-jdk, libhtsjdk-java -Standards-Version: 4.2.1 +Standards-Version: 4.3.0 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 ===================================== @@ -1,10 +1,10 @@ -# Author: Dylan Assi <[email protected]> -# Last-Update: 2018-09-16 +# Author: Dylan Assi <[email protected]> +# Last-Update: 2019-07-04 # These files were downloaded from https://faculty.washington.edu/browning/beagle/ # They should be updated when upstream update them. wget https://faculty.washington.edu/browning/beagle/beagle5_release_notes -O release_notes - wget https://faculty.washington.edu/browning/beagle/beagle_5.0_07Sep18.pdf -O beagle_5.0.pdf - wget https://faculty.washington.edu/browning/beagle/run.beagle.15Sep18.8a0.example -O run.beagle.example - wget http://faculty.washington.edu/browning/beagle/test.15Sep18.8a0.vcf.gz -O test.vcf.gz && \ + wget https://faculty.washington.edu/browning/beagle/beagle_5.0_03Jul19.pdf -O beagle_5.0.pdf + wget https://faculty.washington.edu/browning/beagle/run.beagle.03Jul19.b33.example -O run.beagle.example + wget http://faculty.washington.edu/browning/beagle/test.03Jul19.b33.vcf.gz -O test.vcf.gz && \ gunzip test.vcf.gz ===================================== debian/upstream.docs/beagle_5.0.pdf ===================================== Binary files a/debian/upstream.docs/beagle_5.0.pdf and b/debian/upstream.docs/beagle_5.0.pdf differ ===================================== debian/upstream.docs/run.beagle.example ===================================== @@ -1,47 +1,47 @@ #!/bin/bash -if [ ! -f beagle.15Sep18.8a0.jar ]; then +if [ ! -f beagle.03Jul19.b33.jar ]; then echo - echo "Downloading beagle.15Sep18.8a0.jar" - wget http://faculty.washington.edu/browning/beagle/beagle.15Sep18.8a0.jar + echo "Downloading beagle.03Jul19.b33.jar" + wget http://faculty.washington.edu/browning/beagle/beagle.03Jul19.b33.jar fi -if [ ! -f bref3.15Sep18.8a0.jar ]; then +if [ ! -f bref3.03Jul19.b33.jar ]; then echo - echo "Downloading bref3.15Sep18.8a0.jar" - wget http://faculty.washington.edu/browning/beagle/bref3.15Sep18.8a0.jar + echo "Downloading bref3.03Jul19.b33.jar" + wget http://faculty.washington.edu/browning/beagle/bref3.03Jul19.b33.jar fi echo -if [ ! -f test.15Sep18.8a0.vcf.gz ]; then +if [ ! -f test.03Jul19.b33.vcf.gz ]; then echo - echo "*** Downloading some 1000 Genomes Project data to file: test.15Sep18.8a0.vcf.gz ***" - wget http://faculty.washington.edu/browning/beagle/test.15Sep18.8a0.vcf.gz + echo "*** Downloading some 1000 Genomes Project data to file: test.03Jul19.b33.vcf.gz ***" + wget http://faculty.washington.edu/browning/beagle/test.03Jul19.b33.vcf.gz fi echo -echo "*** Creating test files: ref.15Sep18.8a0.vcf.gz target.15Sep18.8a0.vcf.gz ***" +echo "*** Creating test files: ref.03Jul19.b33.vcf.gz target.03Jul19.b33.vcf.gz ***" echo -zcat test.15Sep18.8a0.vcf.gz | cut -f1-190 | tr '/' '|' | gzip > ref.15Sep18.8a0.vcf.gz -zcat test.15Sep18.8a0.vcf.gz | cut -f1-9,191-200 | gzip > target.15Sep18.8a0.vcf.gz +zcat test.03Jul19.b33.vcf.gz | cut -f1-190 | tr '/' '|' | gzip > ref.03Jul19.b33.vcf.gz +zcat test.03Jul19.b33.vcf.gz | cut -f1-9,191-200 | gzip > target.03Jul19.b33.vcf.gz echo echo "*** Running test analysis with \"gt=\" argument ***" echo -java -jar beagle.15Sep18.8a0.jar gt=test.15Sep18.8a0.vcf.gz out=out.gt +java -jar beagle.03Jul19.b33.jar gt=test.03Jul19.b33.vcf.gz out=out.gt echo echo "*** Running test analysis with \"ref=\" and \"gt=\" arguments ***" echo -java -jar beagle.15Sep18.8a0.jar ref=ref.15Sep18.8a0.vcf.gz gt=target.15Sep18.8a0.vcf.gz out=out.ref +java -jar beagle.03Jul19.b33.jar ref=ref.03Jul19.b33.vcf.gz gt=target.03Jul19.b33.vcf.gz out=out.ref echo echo "*** Making \"bref3\" file ***" echo -java -jar bref3.15Sep18.8a0.jar ref.15Sep18.8a0.vcf.gz > ref.15Sep18.8a0.bref3 +java -jar bref3.03Jul19.b33.jar ref.03Jul19.b33.vcf.gz > ref.03Jul19.b33.bref3 echo echo "*** Running test analysis with \"bref3\" file ***" echo -java -jar beagle.15Sep18.8a0.jar ref=ref.15Sep18.8a0.bref3 gt=target.15Sep18.8a0.vcf.gz out=out.bref3 +java -jar beagle.03Jul19.b33.jar ref=ref.03Jul19.b33.bref3 gt=target.03Jul19.b33.vcf.gz out=out.bref3 View it on GitLab: https://salsa.debian.org/med-team/beagle/compare/f0089aa462b38c9cb6638a144a0424c52697106a...5adf6940dacbff22f6a846600017cc26778a95ef -- View it on GitLab: https://salsa.debian.org/med-team/beagle/compare/f0089aa462b38c9cb6638a144a0424c52697106a...5adf6940dacbff22f6a846600017cc26778a95ef You're receiving this email because of your account on salsa.debian.org.
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