[Blends-commit] [Git][blends-team/med][master] Remove tophat and make sure hisat2 is recommended in all tasks previously mentioning tophat

[Andreas Tille]

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

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