This is an automated email from the git hooks/post-receive script. tille pushed a commit to branch master in repository manta.
commit 28a8d77673515c92cca6de248881a357f5db82f6 Author: Andreas Tille <[email protected]> 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") + -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/manta.git _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
