# HG changeset patch # User bgruening # Date 1361221428 18000 # Node ID 9986482cbb48981e030eccd2af01e76e181b6308 # Parent 7a143c7b3f1b98885f1d19d4c07e97f26940d971 Uploaded diff -r 7a143c7b3f1b -r 9986482cbb48 bismark_methylation_extractor.py --- a/bismark_methylation_extractor.py Tue Nov 13 13:32:56 2012 -0500 +++ b/bismark_methylation_extractor.py Mon Feb 18 16:03:48 2013 -0500 @@ -25,6 +25,8 @@ parser = argparse.ArgumentParser(description='Wrapper for the bismark methylation caller.') # input options + parser.add_argument( '--bismark_path', dest='bismark_path', help='Path to the bismark perl scripts' ) + parser.add_argument( '--infile', help='Input file in SAM format.' ) parser.add_argument( '--single-end', dest='single_end', action="store_true" ) parser.add_argument( '--paired-end', dest='paired_end', action="store_true" ) @@ -70,6 +72,9 @@ # Build methylation extractor command output_dir = tempfile.mkdtemp() cmd = 'bismark_methylation_extractor --no_header -o %s %s %s' + if args.bismark_path: + # add the path to the bismark perl scripts, that is needed for galaxy + cmd = os.path.join(args.bismark_path, cmd) additional_opts = '' # Set up all options diff -r 7a143c7b3f1b -r 9986482cbb48 bismark_wrapper.py --- a/bismark_wrapper.py Tue Nov 13 13:32:56 2012 -0500 +++ b/bismark_wrapper.py Mon Feb 18 16:03:48 2013 -0500 @@ -120,7 +120,7 @@ cmd_index = 'bismark_genome_preparation %s ' % ( tmp_index_dir ) if args.bismark_path: # add the path to the bismark perl scripts, that is needed for galaxy - cmd_index = '%s/%s' % (args.bismark_path, cmd_index) + cmd_index = os.path.join(args.bismark_path, cmd_index) try: tmp = tempfile.NamedTemporaryFile( dir=tmp_index_dir ).name tmp_stderr = open( tmp, 'wb' ) @@ -155,7 +155,7 @@ cmd = 'bismark %(args)s --temp_dir %(tmp_bismark_dir)s -o %(output_dir)s --quiet %(genome_folder)s %(reads)s' if args.bismark_path: # add the path to the bismark perl scripts, that is needed for galaxy - cmd = '%s/%s' % (args.bismark_path, cmd) + cmd = os.path.join(args.bismark_path, cmd) arguments = { 'genome_folder': index_dir, diff -r 7a143c7b3f1b -r 9986482cbb48 tool-data/bowtie2_indices.loc.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/bowtie2_indices.loc.sample Mon Feb 18 16:03:48 2013 -0500 @@ -0,0 +1,37 @@ +#This is a sample file distributed with Galaxy that enables tools +#to use a directory of Bowtie2 indexed sequences data files. You will +#need to create these data files and then create a bowtie_indices.loc +#file similar to this one (store it in this directory) that points to +#the directories in which those files are stored. The bowtie2_indices.loc +#file has this format (longer white space characters are TAB characters): +# +# +# +#So, for example, if you had hg18 indexed stored in +#/depot/data2/galaxy/bowtie2/hg18/, +#then the bowtie2_indices.loc entry would look like this: +# +#hg18 hg18 hg18 /depot/data2/galaxy/bowtie2/hg18/hg18 +# +#and your /depot/data2/galaxy/bowtie2/hg18/ directory +#would contain hg18.*.ebwt files: +# +#-rw-r--r-- 1 james universe 830134 2005-09-13 10:12 hg18.1.ebwt +#-rw-r--r-- 1 james universe 527388 2005-09-13 10:12 hg18.2.ebwt +#-rw-r--r-- 1 james universe 269808 2005-09-13 10:12 hg18.3.ebwt +#...etc... +# +#Your bowtie2_indices.loc file should include an entry per line for each +#index set you have stored. The "file" in the path does not actually +#exist, but it is the prefix for the actual index files. For example: +# +#hg18canon hg18 hg18 Canonical /depot/data2/galaxy/bowtie2/hg18/hg18canon +#hg18full hg18 hg18 Full /depot/data2/galaxy/bowtie2/hg18/hg18full +#/orig/path/hg19 hg19 hg19 /depot/data2/galaxy/bowtie2/hg19/hg19 +#...etc... +# +#Note that for backwards compatibility with workflows, the unique ID of +#an entry must be the path that was in the original loc file, because that +#is the value stored in the workflow for that parameter. That is why the +#hg19 entry above looks odd. New genomes can be better-looking. +# diff -r 7a143c7b3f1b -r 9986482cbb48 tool-data/bowtie_indices.loc.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/bowtie_indices.loc.sample Mon Feb 18 16:03:48 2013 -0500 @@ -0,0 +1,37 @@ +#This is a sample file distributed with Galaxy that enables tools +#to use a directory of Bowtie indexed sequences data files. You will +#need to create these data files and then create a bowtie_indices.loc +#file similar to this one (store it in this directory) that points to +#the directories in which those files are stored. The bowtie_indices.loc +#file has this format (longer white space characters are TAB characters): +# +# +# +#So, for example, if you had hg18 indexed stored in +#/depot/data2/galaxy/bowtie/hg18/, +#then the bowtie_indices.loc entry would look like this: +# +#hg18 hg18 hg18 /depot/data2/galaxy/bowtie/hg18/hg18 +# +#and your /depot/data2/galaxy/bowtie/hg18/ directory +#would contain hg18.*.ebwt files: +# +#-rw-r--r-- 1 james universe 830134 2005-09-13 10:12 hg18.1.ebwt +#-rw-r--r-- 1 james universe 527388 2005-09-13 10:12 hg18.2.ebwt +#-rw-r--r-- 1 james universe 269808 2005-09-13 10:12 hg18.3.ebwt +#...etc... +# +#Your bowtie_indices.loc file should include an entry per line for each +#index set you have stored. The "file" in the path does not actually +#exist, but it is the prefix for the actual index files. For example: +# +#hg18canon hg18 hg18 Canonical /depot/data2/galaxy/bowtie/hg18/hg18canon +#hg18full hg18 hg18 Full /depot/data2/galaxy/bowtie/hg18/hg18full +#/orig/path/hg19 hg19 hg19 /depot/data2/galaxy/bowtie/hg19/hg19 +#...etc... +# +#Note that for backwards compatibility with workflows, the unique ID of +#an entry must be the path that was in the original loc file, because that +#is the value stored in the workflow for that parameter. That is why the +#hg19 entry above looks odd. New genomes can be better-looking. +#