[med-svn] [manta] 01/01: Sort out correct pathes, move demo script to manta-demo package

[Andreas Tille]

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tille pushed a commit to branch master
in repository manta.

commit 28a8d77673515c92cca6de248881a357f5db82f6
Author: Andreas Tille <tille at debian.org>
Date:   Tue May 2 13:37:15 2017 +0200

    Sort out correct pathes, move demo script to manta-demo package
---
 debian/control                           |  9 ++++++---
 debian/manta-demo.install                |  3 ++-
 debian/manta.install                     |  2 +-
 debian/patches/force_debian_pathes.patch | 34 ++++++++++++++++++++++++++++++++
 4 files changed, 43 insertions(+), 5 deletions(-)

diff --git a/debian/control b/debian/control
index 1f8146d..5ae7e5a 100644
--- a/debian/control
+++ b/debian/control
@@ -28,7 +28,9 @@ Package: manta
 Architecture: any
 Depends: ${shlibs:Depends},
          ${misc:Depends},
-         ${python:Depends}
+         ${python:Depends},
+         tabix,
+         samtools
 Description: structural variant and indel caller for mapped sequencing data
  Manta calls structural variants (SVs) and indels from mapped paired-end
  sequencing reads. It is optimized for analysis of germline variation in
@@ -51,7 +53,7 @@ Description: structural variant and indel caller for mapped sequencing data
 Package: manta-demo
 Architecture: all
 Depends: ${misc:Depends},
-Suggests: manta
+         manta
 Description: demo data for manta structural variant and indel caller
  Manta calls structural variants (SVs) and indels from mapped paired-end
  sequencing reads. It is optimized for analysis of germline variation in
@@ -71,4 +73,5 @@ Description: demo data for manta structural variant and indel caller
  mappings from BAM or CRAM files and reports all SV and indel inferences
  in VCF 4.1 format.
  .
- This package contains some data for testing manta.
+ This package contains some data for testing manta as well as an
+ example script.
diff --git a/debian/manta-demo.install b/debian/manta-demo.install
index 7fbffb9..00325b4 100644
--- a/debian/manta-demo.install
+++ b/debian/manta-demo.install
@@ -1 +1,2 @@
-usr/share/demo/manta/data	usr/share/doc/manta
+usr/share/demo/manta/data
+debian/bin/runMantaWorkflowDemo	usr/bin
diff --git a/debian/manta.install b/debian/manta.install
index 34505b1..8c4830c 100644
--- a/debian/manta.install
+++ b/debian/manta.install
@@ -1,4 +1,4 @@
 usr/lib/manta
 usr/lib/python/*	usr/share/manta
 usr/bin			usr
-debian/bin		usr
+debian/bin/configManta	usr/bin
diff --git a/debian/patches/force_debian_pathes.patch b/debian/patches/force_debian_pathes.patch
index 88dd987..a4ccf05 100644
--- a/debian/patches/force_debian_pathes.patch
+++ b/debian/patches/force_debian_pathes.patch
@@ -14,3 +14,37 @@ Description: libexec seems Redhat specific, in Debian the according files can
  
  # paths w/o architecture dependency
  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
+ 
+         alignerMode = "isaac"
+ 
+-        libexecDir=os.path.abspath(os.path.join(scriptDir,"@THIS_RELATIVE_LIBEXECDIR@"))
++        libexecDir='/usr/lib/manta' # no idea why this is expanded to /usr/share/manta in cmake build
+         assert os.path.isdir(libexecDir)
+ 
+-        bgzipBin=joinFile(libexecDir,exeFile("bgzip"))
+-        htsfileBin=joinFile(libexecDir,exeFile("htsfile"))
+-        tabixBin=joinFile(libexecDir,exeFile("tabix"))
+-        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"))
++        tabixBin=joinFile(bindir,exeFile("tabix"))
++        samtoolsBin=joinFile(bindir,exeFile("samtools"))
+ 
+         mantaStatsBin=joinFile(libexecDir,exeFile("GetAlignmentStats"))
+         mantaMergeStatsBin=joinFile(libexecDir,exeFile("MergeAlignmentStats"))
+--- a/src/demo/runMantaWorkflowDemo.py
++++ b/src/demo/runMantaWorkflowDemo.py
+@@ -32,7 +32,7 @@ def main() :
+     # initialize paths:
+     #
+     scriptDir=os.path.abspath(os.path.dirname(__file__))
+-    demoDir=os.path.abspath(os.path.join(scriptDir,os.pardir,"share","demo","manta"))
++    demoDir=os.path.abspath(os.path.join(scriptDir,os.pardir,"demo","manta"))
+     dataDir=os.path.join(demoDir,"data")
+     expectedDir=os.path.join(demoDir,"expectedResults")
+ 

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