Andreas Tille pushed to branch master at Debian Blends Team / med
Commits:
97d88760 by Andreas Tille at 2019-11-27T10:14:52Z
Remove tophat and make sure hisat2 is recommended in all tasks previously
mentioning tophat
- - - - -
3 changed files:
- tasks/bio
- tasks/bio-ngs
- tasks/cloud
Changes:
=====================================
tasks/bio
=====================================
@@ -46,9 +46,7 @@ Remark: Dead upstream
old unmaintained version remained at code.google.com. Please drop the
maintainer a note if you have any news of this project.
-Recommends: boxshade, fastx-toolkit, gff2aplot, muscle, sim4, sibsim4,
tabix, tophat, wise
-
-Suggest: tophat-recondition
+Recommends: boxshade, fastx-toolkit, gff2aplot, muscle, sim4, sibsim4,
tabix, wise
Recommends: maqview
=====================================
tasks/bio-ngs
=====================================
@@ -22,7 +22,6 @@ Recommends:
sra-toolkit,
ssake,
tabix,
- tophat,
bcftools,
vcftools,
velvet
@@ -219,8 +218,6 @@ Recommends: sra-toolkit
Recommends: stringtie
-Recommends: tophat
-
Recommends: transrate-tools
Recommends: trimmomatic
=====================================
tasks/cloud
=====================================
@@ -31,7 +31,7 @@ Recommends: bamtools, bedtools, fastx-toolkit, flexbar,
picard-tools, samtools,
Comment: Processing
Recommends: anfo, cufflinks, bowtie, bowtie2, bwa, last-align, maq, perm,
- tophat, smalt, soapdenovo, soapdenovo2
+ hisat2, smalt, soapdenovo, soapdenovo2
Comment: Aligners
Recommends: abyss, mapsembler2, idba, minia, mira-assembler, ssake, velvet
View it on GitLab:
https://salsa.debian.org/blends-team/med/commit/97d887604435dda6527a8a213d71ed2ae940562c
--
View it on GitLab:
https://salsa.debian.org/blends-team/med/commit/97d887604435dda6527a8a213d71ed2ae940562c
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