Skip to content

Commit

Permalink
fixed path to pysam
Browse files Browse the repository at this point in the history
  • Loading branch information
@AndreasHeger
AndreasHeger committed Aug 22, 2012
1 parent a954214 commit e23ebc3
Show file tree
Hide file tree
Showing 8 changed files with 22 additions and 20 deletions.
3 changes: 3 additions & 0 deletions Pipeline.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -964,6 +964,9 @@ def peekParameters( workingdir, pipeline ):
dirname = os.path.dirname( __file__ )
pipeline = os.path.join( dirname, pipeline )
assert os.path.exists( pipeline ), "can't find pipeline source %s" % pipeline
if workingdir == "":
return {}

assert os.path.exists( workingdir ), "can't find working dir %s" % workingdir

process = subprocess.Popen( "python %s -f -v 0 dump" % pipeline,
Expand Down
6 changes: 3 additions & 3 deletions _bam2bam.pyxbld
View file
Original file line number Diff line number Diff line change
Expand Up @@ -7,10 +7,10 @@ def make_ext(modname, pyxfilename):
return Extension(name = modname,
sources=[pyxfilename],
#library_dirs + libraries does not work as it would require csamtools.so to start with lib
#library_dirs = ['/ifs/devel/pysam/pysam-0.4/build/lib.linux-x86_64-2.7'],
#library_dirs = ['/ifs/devel/pysam-0.4/build/lib.linux-x86_64-2.7'],
#libraries= ['csamtools'],
extra_link_args=[ os.path.join( dirname, "csamtools.so")],
include_dirs = ['/ifs/devel/pysam/pysam/samtools',
'/ifs/devel/pysam/pysam/pysam',
include_dirs = ['/ifs/devel/pysam/samtools',
'/ifs/devel/pysam/pysam',
] )

6 changes: 3 additions & 3 deletions _bam2bed.pyxbld
View file
Original file line number Diff line number Diff line change
Expand Up @@ -7,10 +7,10 @@ def make_ext(modname, pyxfilename):
return Extension(name = modname,
sources=[pyxfilename],
#library_dirs + libraries does not work as it would require csamtools.so to start with lib
#library_dirs = ['/ifs/devel/pysam/pysam-0.4/build/lib.linux-x86_64-2.7'],
#library_dirs = ['/ifs/devel/pysam-0.4/build/lib.linux-x86_64-2.7'],
#libraries= ['csamtools'],
extra_link_args=[ os.path.join( dirname, "csamtools.so")],
include_dirs = ['/ifs/devel/pysam/pysam/samtools',
'/ifs/devel/pysam/pysam/pysam',
include_dirs = ['/ifs/devel/pysam/samtools',
'/ifs/devel/pysam/pysam',
] )

6 changes: 3 additions & 3 deletions _bam2geneprofile.pyxbld
View file
Original file line number Diff line number Diff line change
Expand Up @@ -7,10 +7,10 @@ def make_ext(modname, pyxfilename):
return Extension(name = modname,
sources=[pyxfilename],
#library_dirs + libraries does not work as it would require csamtools.so to start with lib
#library_dirs = ['/ifs/devel/pysam/pysam-0.4/build/lib.linux-x86_64-2.7'],
#library_dirs = ['/ifs/devel/pysam-0.4/build/lib.linux-x86_64-2.7'],
#libraries= ['csamtools'],
extra_link_args=[ os.path.join( dirname, "csamtools.so")],
include_dirs = ['/ifs/devel/pysam/pysam/samtools',
'/ifs/devel/pysam/pysam/pysam',
include_dirs = ['/ifs/devel/pysam/samtools',
'/ifs/devel/pysam/pysam',
] )

6 changes: 3 additions & 3 deletions _bam2peakshape.pyxbld
View file
Original file line number Diff line number Diff line change
Expand Up @@ -7,10 +7,10 @@ def make_ext(modname, pyxfilename):
return Extension(name = modname,
sources=[pyxfilename],
#library_dirs + libraries does not work as it would require csamtools.so to start with lib
#library_dirs = ['/ifs/devel/pysam/pysam-0.4/build/lib.linux-x86_64-2.7'],
#library_dirs = ['/ifs/devel/pysam-0.4/build/lib.linux-x86_64-2.7'],
#libraries= ['csamtools'],
extra_link_args=[ os.path.join( dirname, "csamtools.so")],
include_dirs = ['/ifs/devel/pysam/pysam/samtools',
'/ifs/devel/pysam/pysam/pysam',
include_dirs = ['/ifs/devel/pysam/samtools',
'/ifs/devel/pysam/pysam',
] )

6 changes: 3 additions & 3 deletions _bam2stats.pyxbld
View file
Original file line number Diff line number Diff line change
Expand Up @@ -7,10 +7,10 @@ def make_ext(modname, pyxfilename):
return Extension(name = modname,
sources=[pyxfilename],
#library_dirs + libraries does not work as it would require csamtools.so to start with lib
#library_dirs = ['/ifs/devel/pysam/pysam-0.4/build/lib.linux-x86_64-2.7'],
#library_dirs = ['/ifs/devel/pysam-0.4/build/lib.linux-x86_64-2.7'],
#libraries= ['csamtools'],
extra_link_args=[ os.path.join( dirname, "csamtools.so")],
include_dirs = ['/ifs/devel/pysam/pysam/samtools',
'/ifs/devel/pysam/pysam/pysam',
include_dirs = ['/ifs/devel/pysam/samtools',
'/ifs/devel/pysam/pysam',
] )

6 changes: 3 additions & 3 deletions _rnaseq_bams2bam.pyxbld
View file
Original file line number Diff line number Diff line change
Expand Up @@ -7,10 +7,10 @@ def make_ext(modname, pyxfilename):
return Extension(name = modname,
sources=[pyxfilename],
#library_dirs + libraries does not work as it would require csamtools.so to start with lib
#library_dirs = ['/ifs/devel/pysam/pysam-0.4/build/lib.linux-x86_64-2.7'],
#library_dirs = ['/ifs/devel/pysam-0.4/build/lib.linux-x86_64-2.7'],
#libraries= ['csamtools'],
extra_link_args=[ os.path.join( dirname, "csamtools.so")],
include_dirs = ['/ifs/devel/pysam/pysam/samtools',
'/ifs/devel/pysam/pysam/pysam',
include_dirs = ['/ifs/devel/pysam/samtools',
'/ifs/devel/pysam/pysam',
] )

3 changes: 1 addition & 2 deletions pipeline_chipseq.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -216,7 +216,7 @@
###################################################
import Pipeline as P
P.getParameters(
["%s/pipeline.ini" % __file__[:-len(".py")],
["%s/pipeline.ini" % os.path.splitext(__file__)[0],
"../pipeline.ini",
"pipeline.ini" ],
defaults = {
Expand Down Expand Up @@ -384,7 +384,6 @@ def loadReadCounts( infiles, outfile ):
###################################################################
## Mapping
###################################################################

if PARAMS["mapping_mapper"] == "bowtie":

############################################################
Expand Down

0 comments on commit e23ebc3

Please sign in to comment.