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tille pushed a commit to branch master
in repository manta.
commit eef67e3bdcad69581caeecf52f2aafe6ba63d723
Author: Andreas Tille <tille at debian.org>
Date: Tue May 2 16:36:15 2017 +0200
htsfile is now in tabix 1.4-2
---
debian/control | 2 +-
debian/patches/force_debian_pathes.patch | 5 ++---
2 files changed, 3 insertions(+), 4 deletions(-)
diff --git a/debian/control b/debian/control
index 7410bb4..b36a168 100644
--- a/debian/control
+++ b/debian/control
@@ -30,7 +30,7 @@ Architecture: any
Depends: ${shlibs:Depends},
${misc:Depends},
${python:Depends},
- tabix,
+ tabix (>= 1.4-2),
samtools
Description: structural variant and indel caller for mapped sequencing data
Manta calls structural variants (SVs) and indels from mapped paired-end
diff --git a/debian/patches/force_debian_pathes.patch b/debian/patches/force_debian_pathes.patch
index a4ccf05..cbc6866 100644
--- a/debian/patches/force_debian_pathes.patch
+++ b/debian/patches/force_debian_pathes.patch
@@ -16,7 +16,7 @@ Description: libexec seems Redhat specific, in Debian the according files can
set(THIS_PYTHON_LIBDIR "${CMAKE_INSTALL_PREFIX}/lib/python")
--- a/src/python/lib/mantaOptions.py
+++ b/src/python/lib/mantaOptions.py
-@@ -79,13 +79,15 @@ class MantaWorkflowOptionsBase(Configure
+@@ -79,13 +79,14 @@ class MantaWorkflowOptionsBase(Configure
alignerMode = "isaac"
@@ -30,8 +30,7 @@ Description: libexec seems Redhat specific, in Debian the according files can
- samtoolsBin=joinFile(libexecDir,exeFile("samtools"))
+ bindir = '/usr/bin'
+ bgzipBin=joinFile(bindir,exeFile("bgzip"))
-+ # FIXME: htsfile is NOT build by the Debian package - needs to be done
-+ # htsfileBin=joinFile(libexecDir,exeFile("htsfile"))
++ htsfileBin=joinFile(bindir,exeFile("htsfile"))
+ tabixBin=joinFile(bindir,exeFile("tabix"))
+ samtoolsBin=joinFile(bindir,exeFile("samtools"))
--
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