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#75 upgrade pysam to 0.9.x and htslib/samtools to 1.5

0.2
open
Wolfgang Maier
enhancement (53)
2017-06-23
2015-11-11
Wolfgang Maier
No

this will allow us to drop samtools 0.1.19 code altogether and to just link against the already compiled MiModD htslib, which, in turn, will reduce download size and installation time

Discussion

  • Wolfgang Maier

    Wolfgang Maier - 2015-11-11
    • Milestone: 0.1.7.2 --> 0.1.8
     

  • Wolfgang Maier

    Wolfgang Maier - 2015-11-17
    • Milestone: 0.1.8 --> 0.2
     

  • Wolfgang Maier

    Wolfgang Maier - 2016-10-15
    • summary: upgrade pysam to 0.8.x --> upgrade pysam to 0.9.x and htslib/samtools to 1.3
    • Description has changed:

    Diff:

    --- old
+++ new
@@ -0,0 +1 @@
+this will allow us to drop samtools 0.1.19 code altogether and to just link against the already compiled MiModD htslib, which, in turn, will reduce download size and installation time
     

  • Wolfgang Maier

    Wolfgang Maier - 2017-06-23
    • summary: upgrade pysam to 0.9.x and htslib/samtools to 1.3 --> upgrade pysam to 0.9.x and htslib/samtools to 1.5
     

  • Wolfgang Maier

    Wolfgang Maier - 2017-06-23

    upgrading to samtools 1.3+ will in addition let Galaxy users run the current bowtie2 wrapper available from the toolshed with MiModD's copy of samtools (due to a bug in the handling of the -O/-T option combination in the samtools 1.2 sort command this is currently not possible)

     

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