[med-svn] [Git][med-team/bcbio][master] Refinements after introducing gsort

[Steffen Möller]

Steffen Möller pushed to branch master at Debian Med / bcbio


Commits:
c2788402 by Steffen Moeller at 2020-11-23T16:14:38+01:00
Refinements after introducing gsort

- - - - -


3 changed files:

- debian/control
- + debian/patches/fixeFreetypePreload.patch
- debian/patches/series


Changes:

=====================================
debian/control
=====================================
@@ -31,8 +31,10 @@ Build-Depends: debhelper-compat (= 13),
                freebayes <!nocheck>,
                gffread <!nocheck>,
                grabix <!nocheck>,
+               gsort <!nocheck>,
                hisat2 <!nocheck>,
                hts-nim-tools <!nocheck>,
+               libfreetype6 <!nocheck>,
                lumpy-sv <!nocheck>,
                mosdepth <!nocheck>,
                multiqc <!nocheck>,
@@ -57,6 +59,7 @@ Build-Depends: debhelper-compat (= 13),
                r-bioc-degreport <!nocheck>,
                r-cran-tidyverse <!nocheck>,
                r-bioc-tximport <!nocheck>,
+               r-other-wasabi <!nocheck>,
                salmon <!nocheck>,
                samblaster <!nocheck>,
                samtools <!nocheck>,
@@ -96,6 +99,8 @@ Depends: ${python3:Depends},
          python3-tornado
 Recommends:
          cnvkit,
+         gsort,
+         libfreetype6,
          lumpy-sv,
          mosdepth,
          multiqc,
@@ -106,6 +111,7 @@ Recommends:
          python3-seqcluster,
          python3-statsmodels,
          python3-tabulate,
+         r-other-wasabi,
          seqan-apps,
          vcfanno,
          vt


=====================================
debian/patches/fixeFreetypePreload.patch
=====================================
@@ -0,0 +1,15 @@
+Author: Steffen Moeller
+Description: The location of the freetype library on Debian is not where upstream expected it.
+Index: bcbio/bcbio/utils.py
+===================================================================
+--- bcbio.orig/bcbio/utils.py
++++ bcbio/bcbio/utils.py
+@@ -911,7 +911,7 @@ def java_freetype_fix():
+ 
+     Cheap workaround with LD_PRELOAD, I don't know a better one.
+     """
+-    return "export LD_PRELOAD=%s/lib/libfreetype.so && " % os.path.dirname(get_bcbio_bin())
++    return "export LD_PRELOAD=/usr/lib/$(dpkg-architecture -qDEB_HOST_GNU_TYPE)/libfreetype.so.6 && "
+ 
+ def is_gzipped(fname):
+     _, ext = os.path.splitext(fname)


=====================================
debian/patches/series
=====================================
@@ -7,3 +7,4 @@ pythonpaths.patch
 hts_nim_tools.patch
 collectionsAbc.patch
 cnvkitPath.patch
+fixeFreetypePreload.patch



View it on GitLab: https://salsa.debian.org/med-team/bcbio/-/commit/c27884029a9a7e15d9292117572dd116c1a143ca

-- 
View it on GitLab: https://salsa.debian.org/med-team/bcbio/-/commit/c27884029a9a7e15d9292117572dd116c1a143ca
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