Pranav Ballaney pushed to branch master at Debian Med / gasic
Commits: a0b828af by Pranav Ballaney at 2020-05-12T17:40:51+05:30 Remove unnecessary example files - - - - - de364d47 by Pranav Ballaney at 2020-05-13T01:31:49+05:30 Fix mason_simulator arguments - - - - - e611aaf5 by Pranav Ballaney at 2020-05-13T02:38:05+05:30 Add more autopkgtests - - - - - c42123d6 by Pranav Ballaney at 2020-05-13T02:39:51+05:30 Remove removed binaries from include-binaries - - - - - ac007039 by Pranav Ballaney at 2020-05-13T15:10:46+05:30 Merge branch 'master' of https://salsa.debian.org/med-team/gasic - - - - - f2779eb9 by Pranav Ballaney at 2020-05-13T15:18:46+05:30 Update changelog - - - - - 11 changed files: - debian/changelog - debian/patches/use_seqan_mason.patch - debian/source/include-binaries - − debian/tests/data/genomes/dwv.fasta-e.gz - − debian/tests/data/genomes/dwv.fasta.fai.gz - − debian/tests/data/genomes/vdv-1-dwv-5.fasta.fai.gz - − debian/tests/data/genomes/vdv-1-dwv-9.fasta.fai.gz - − debian/tests/data/genomes/vdv1.fasta.fai.gz - + debian/tests/data/names - − debian/tests/data/names.gz - debian/tests/run-unit-test Changes: ===================================== debian/changelog ===================================== @@ -1,3 +1,12 @@ +gasic (0.0.r19-7) UNRELEASED; urgency=medium + + * Remove unnecessary example files + * Fix mason_simulator arguments + * Add more autopkgtests + * Remove removed binaries from include-binaries + + -- Pranav Ballaney <[email protected]> Wed, 13 May 2020 15:13:02 +0530 + gasic (0.0.r19-6) unstable; urgency=medium * Team upload ===================================== debian/patches/use_seqan_mason.patch ===================================== @@ -18,7 +18,7 @@ Description: since there is a name conflict with mason and the Debian package + reportbug gasic +to propose enhancements. +""" % (out,ref)) -+ command = "/usr/lib/seqan/bin/mason_simulator illumina --illumina-read-length 10000 -o %s %s"%(out,ref) ++ command = "/usr/lib/seqan/bin/mason_simulator --seq-technology illumina -n 10000 --illumina-read-length 72 -o %s -ir %s"%(out,ref) print("Executing:",command) os.system(command) # remove the needless SAM file ===================================== debian/source/include-binaries ===================================== @@ -1,11 +1,4 @@ -debian/tests/data/names.gz -debian/tests/data/genomes/vdv1.fasta.fai.gz +debian/tests/data/genomes/dwv.fasta.gz debian/tests/data/genomes/vdv1.fasta.gz debian/tests/data/genomes/vdv1dwv9.fasta.gz debian/tests/data/genomes/vdv1dwv5.fasta.gz -debian/tests/data/genomes/vdv-1-dwv-9.fasta.fai.gz -debian/tests/data/genomes/vdv-1-dwv-5.fasta.fai.gz -debian/tests/data/genomes/dwv.fasta-e.gz -debian/tests/data/genomes/dwv.fasta.fai.gz -debian/tests/data/genomes/dwv.fasta.gz -debian/tests/data/reads/SRR059298_subset.fastq.gz ===================================== debian/tests/data/genomes/dwv.fasta-e.gz deleted ===================================== Binary files a/debian/tests/data/genomes/dwv.fasta-e.gz and /dev/null differ ===================================== debian/tests/data/genomes/dwv.fasta.fai.gz deleted ===================================== Binary files a/debian/tests/data/genomes/dwv.fasta.fai.gz and /dev/null differ ===================================== debian/tests/data/genomes/vdv-1-dwv-5.fasta.fai.gz deleted ===================================== Binary files a/debian/tests/data/genomes/vdv-1-dwv-5.fasta.fai.gz and /dev/null differ ===================================== debian/tests/data/genomes/vdv-1-dwv-9.fasta.fai.gz deleted ===================================== Binary files a/debian/tests/data/genomes/vdv-1-dwv-9.fasta.fai.gz and /dev/null differ ===================================== debian/tests/data/genomes/vdv1.fasta.fai.gz deleted ===================================== Binary files a/debian/tests/data/genomes/vdv1.fasta.fai.gz and /dev/null differ ===================================== debian/tests/data/names ===================================== @@ -0,0 +1,4 @@ +dwv +vdv1 +vdv1dwv5 +vdv1dwv9 ===================================== debian/tests/data/names.gz deleted ===================================== Binary files a/debian/tests/data/names.gz and /dev/null differ ===================================== debian/tests/run-unit-test ===================================== @@ -15,13 +15,33 @@ cd "${AUTOPKGTEST_TMP}" gunzip -r * +echo -e "\e[93m\e[1mTest 0: Create Genome Indices\e[0m" cd genomes +bwa index dwv.fasta +bwa index vdv1.fasta +bwa index vdv1dwv9.fasta +bwa index vdv1dwv5.fasta +cd .. +echo -e "\e[92m\e[1mPassed\e[0m" +echo -bowtie-build dwv.fasta dwv.fasta -bowtie-build vdv1.fasta vdv1.fasta -bowtie-build vdv1dwv9.fasta vdv1dwv9.fasta -bowtie-build vdv1dwv5.fasta vdv1dwv5.fasta +echo -e "\e[93m\e[1mTest 1: run_mappers\e[0m" +run_mappers names reads/SRR059298_subset.fastq -i ./genomes/%s.fasta -o ./SAM/mapped_%s.sam -m bwa +echo -e "\e[92m\e[1mPassed\e[0m" +echo -cd .. +echo -e "\e[93m\e[1mTest 2: create_matrix\e[0m" +create_matrix names -s mason_illumina -m bwa -r genomes/%s.fasta -i genomes/%s.fasta -t ./SAM +echo -e "\e[92m\e[1mPassed\e[0m" +echo + +echo -e "\e[93m\e[1mTest 3: correct_abundances\e[0m" +correct_abundances names -s ./SAM/mapped_%s.sam -m similarity_matrix.npy -o results.txt +echo -e "\e[92m\e[1mPassed\e[0m" +echo + +echo -e "\e[93m\e[1mTest 4: quality_check\e[0m" +quality_check ./SAM/mapped_vdv1.sam +echo -e "\e[92m\e[1mPassed\e[0m" +echo -run_mappers names reads/SRR059298_subset.fastq -i ./genomes/%s.fasta -o ./SAM/mapped_%s.sam -m bowtie View it on GitLab: https://salsa.debian.org/med-team/gasic/-/compare/0c51555761bd86d7ad4110ae12820383c0707064...f2779eb9678c3d88f643a61755f330dcd35aefd9 -- View it on GitLab: https://salsa.debian.org/med-team/gasic/-/compare/0c51555761bd86d7ad4110ae12820383c0707064...f2779eb9678c3d88f643a61755f330dcd35aefd9 You're receiving this email because of your account on salsa.debian.org.
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