4 new changesets in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/326c1dd14ae3/ changeset: r5408:326c1dd14ae3 user: natefoo date: 2011-04-18 22:40:43 summary: Scramble script for bx-python on Solaris (needs some C99 defines). affected #: 1 file (890 bytes) --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/scripts/scramble/scripts/bx_python-solaris.py Mon Apr 18 16:40:43 2011 -0400 @@ -0,0 +1,33 @@ +import os, sys + +# change back to the build dir +if os.path.dirname( sys.argv[0] ) != "": + os.chdir( os.path.dirname( sys.argv[0] ) ) + +# find setuptools +sys.path.append( os.path.join( '..', '..', '..', 'lib' ) ) +from scramble_lib import * + +tag = get_tag() # get the tag +get_deps() # require any dependent eggs +clean() # clean up any existing stuff (could happen if you run scramble.py by hand) + +# reset args for distutils +me = sys.argv[0] +sys.argv = [ me ] +sys.argv.append( "egg_info" ) +if tag is not None: + sys.argv.append( "--tag-build=%s" %tag ) +# svn revision (if any) is handled directly in tag-build +sys.argv.append( "--no-svn-revision" ) +sys.argv.append( "bdist_egg" ) + +# apply patches (if any) +apply_patches() + +cc = get_solaris_compiler() +if cc == 'cc': + os.environ['CFLAGS'] = '-xc99=all -D_X_OPEN_SOURCE=600 -D_XPG6=1' + +# do it +execfile( "setup.py", globals(), locals() ) http://bitbucket.org/galaxy/galaxy-central/changeset/77889e2ca8c1/ changeset: r5409:77889e2ca8c1 user: natefoo date: 2011-04-18 22:41:38 summary: Just build on Solaris 10 for sparc. Apologies to anyone running a 9+ year old OS. ;) affected #: 1 file (1010 bytes) --- a/dist-eggs.ini Mon Apr 18 16:40:43 2011 -0400 +++ b/dist-eggs.ini Mon Apr 18 16:41:38 2011 -0400 @@ -29,14 +29,6 @@ py2.4-solaris-2.10-i86pc_64-ucs2 = thumper.bx.psu.edu /afs/bx.psu.edu/project/pythons/solaris-2.10-i86pc_64-ucs2/bin/python2.4 py2.5-solaris-2.10-i86pc_64-ucs2 = thumper.bx.psu.edu /afs/bx.psu.edu/project/pythons/solaris-2.10-i86pc_64-ucs2/bin/python2.5 py2.6-solaris-2.10-i86pc_64-ucs2 = thumper.bx.psu.edu /afs/bx.psu.edu/project/pythons/solaris-2.10-i86pc_64-ucs2/bin/python2.6 -py2.4-solaris-2.8-sun4u_32-ucs2 = troegs.bx.psu.edu /afs/bx.psu.edu/project/pythons/solaris-2.8-sun4u_32-ucs2/bin/python2.4 -py2.5-solaris-2.8-sun4u_32-ucs2 = troegs.bx.psu.edu /afs/bx.psu.edu/project/pythons/solaris-2.8-sun4u_32-ucs2/bin/python2.5 -py2.6-solaris-2.8-sun4u_32-ucs2 = troegs.bx.psu.edu /afs/bx.psu.edu/project/pythons/solaris-2.8-sun4u_32-ucs2/bin/python2.6 -py2.4-solaris-2.8-sun4u_64-ucs2 = troegs.bx.psu.edu /afs/bx.psu.edu/project/pythons/solaris-2.8-sun4u_64-ucs2/bin/python2.4 -py2.5-solaris-2.8-sun4u_64-ucs2 = troegs.bx.psu.edu /afs/bx.psu.edu/project/pythons/solaris-2.8-sun4u_64-ucs2/bin/python2.5 -py2.6-solaris-2.8-sun4u_64-ucs2 = troegs.bx.psu.edu /afs/bx.psu.edu/project/pythons/solaris-2.8-sun4u_64-ucs2/bin/python2.6 - -; pysam doesn't build on solaris < 10, so for it alone we need these hosts py2.4-solaris-2.10-sun4u_32-ucs2 = early.bx.psu.edu /afs/bx.psu.edu/project/pythons/solaris-2.8-sun4u_32-ucs2/bin/python2.4 py2.5-solaris-2.10-sun4u_32-ucs2 = early.bx.psu.edu /afs/bx.psu.edu/project/pythons/solaris-2.8-sun4u_32-ucs2/bin/python2.5 py2.6-solaris-2.10-sun4u_32-ucs2 = early.bx.psu.edu /afs/bx.psu.edu/project/pythons/solaris-2.8-sun4u_32-ucs2/bin/python2.6 @@ -69,9 +61,9 @@ py2.4-solaris-i86pc = py2.4-solaris-2.10-i86pc_32-ucs2 py2.4-solaris-2.10-i86pc_64-ucs2 py2.5-solaris-i86pc = py2.5-solaris-2.10-i86pc_32-ucs2 py2.5-solaris-2.10-i86pc_64-ucs2 py2.6-solaris-i86pc = py2.6-solaris-2.10-i86pc_32-ucs2 py2.6-solaris-2.10-i86pc_64-ucs2 -py2.4-solaris-sun4u = py2.4-solaris-2.8-sun4u_32-ucs2 py2.4-solaris-2.8-sun4u_64-ucs2 -py2.5-solaris-sun4u = py2.5-solaris-2.8-sun4u_32-ucs2 py2.5-solaris-2.8-sun4u_64-ucs2 -py2.6-solaris-sun4u = py2.6-solaris-2.8-sun4u_32-ucs2 py2.6-solaris-2.8-sun4u_64-ucs2 +py2.4-solaris-sun4u = py2.4-solaris-2.10-sun4u_32-ucs2 py2.4-solaris-2.10-sun4u_64-ucs2 +py2.5-solaris-sun4u = py2.5-solaris-2.10-sun4u_32-ucs2 py2.5-solaris-2.10-sun4u_64-ucs2 +py2.6-solaris-sun4u = py2.6-solaris-2.10-sun4u_32-ucs2 py2.6-solaris-2.10-sun4u_64-ucs2 py2.4-solaris = py2.4-solaris-i86pc py2.4-solaris-sun4u py2.5-solaris = py2.5-solaris-i86pc py2.5-solaris-sun4u py2.6-solaris = py2.6-solaris-i86pc py2.6-solaris-sun4u @@ -97,5 +89,4 @@ [ignore] GeneTrack = py2.4 python-daemon = py2.4 -pysam = py2.4-solaris-2.8-sun4u_32-ucs2 py2.5-solaris-2.8-sun4u_32-ucs2 py2.6-solaris-2.8-sun4u_32-ucs2 py2.4-solaris-2.8-sun4u_64-ucs2 py2.5-solaris-2.8-sun4u_64-ucs2 py2.6-solaris-2.8-sun4u_64-ucs2 -ctypes = py2.5-linux-i686-ucs2 py2.5-linux-i686-ucs4 py2.6-linux-i686-ucs2 py2.6-linux-i686-ucs4 py2.5-linux-x86_64-ucs2 py2.5-linux-x86_64-ucs4 py2.6-linux-x86_64-ucs2 py2.6-linux-x86_64-ucs4 py2.5-macosx-10.3-fat-ucs2 py2.6-macosx-10.3-fat-ucs2 py2.6-macosx-10.6-universal-ucs2 py2.5-solaris-2.10-i86pc_32-ucs2 py2.6-solaris-2.10-i86pc_32-ucs2 py2.5-solaris-2.10-i86pc_64-ucs2 py2.6-solaris-2.10-i86pc_64-ucs2 py2.5-solaris-2.8-sun4u_32-ucs2 py2.6-solaris-2.8-sun4u_32-ucs2 py2.5-solaris-2.8-sun4u_64-ucs2 py2.6-solaris-2.8-sun4u_64-ucs2 +ctypes = py2.5-linux-i686-ucs2 py2.5-linux-i686-ucs4 py2.6-linux-i686-ucs2 py2.6-linux-i686-ucs4 py2.5-linux-x86_64-ucs2 py2.5-linux-x86_64-ucs4 py2.6-linux-x86_64-ucs2 py2.6-linux-x86_64-ucs4 py2.5-macosx-10.3-fat-ucs2 py2.6-macosx-10.3-fat-ucs2 py2.6-macosx-10.6-universal-ucs2 py2.5-solaris-2.10-i86pc_32-ucs2 py2.6-solaris-2.10-i86pc_32-ucs2 py2.5-solaris-2.10-i86pc_64-ucs2 py2.6-solaris-2.10-i86pc_64-ucs2 py2.5-solaris-2.10-sun4u_32-ucs2 py2.6-solaris-2.10-sun4u_32-ucs2 py2.5-solaris-2.10-sun4u_64-ucs2 py2.6-solaris-2.10-sun4u_64-ucs2 http://bitbucket.org/galaxy/galaxy-central/changeset/0194ab30a730/ changeset: r5410:0194ab30a730 user: natefoo date: 2011-04-18 22:42:12 summary: Update bx-python to the tip. affected #: 1 file (0 bytes) --- a/eggs.ini Mon Apr 18 16:41:38 2011 -0400 +++ b/eggs.ini Mon Apr 18 16:42:12 2011 -0400 @@ -66,7 +66,7 @@ psycopg2 = _8.4.2_static pysqlite = _3.6.17_static MySQL_python = _5.1.41_static -bx_python = _14b6a6c95da6 +bx_python = _494c2d1d68b3 GeneTrack = _dev_48da9e998f0caf01c5be731e926f4b0481f658f0 SQLAlchemy = _dev_r6498 pysam = _kanwei_ae2bd50d9945 http://bitbucket.org/galaxy/galaxy-central/changeset/20782642367a/ changeset: r5411:20782642367a user: natefoo date: 2011-04-18 22:43:35 summary: merge affected #: 2 files (759 bytes) --- a/tools/samtools/bam_to_sam.py Mon Apr 18 16:42:12 2011 -0400 +++ b/tools/samtools/bam_to_sam.py Mon Apr 18 16:43:35 2011 -0400 @@ -21,6 +21,7 @@ parser = optparse.OptionParser() parser.add_option( '', '--input1', dest='input1', help='The input SAM dataset' ) parser.add_option( '', '--output1', dest='output1', help='The output BAM dataset' ) + parser.add_option( '', '--header', dest='header', action='store_true', default=False, help='Write SAM Header' ) ( options, args ) = parser.parse_args() # output version # of tool @@ -87,7 +88,11 @@ try: # Extract all alignments from the input BAM file to SAM format ( since no region is specified, all the alignments will be extracted ). - command = 'samtools view -o %s %s' % ( options.output1, tmp_sorted_aligns_file_name ) + if options.header: + view_options = "-h" + else: + view_options = "" + command = 'samtools view %s -o %s %s' % ( view_options, options.output1, tmp_sorted_aligns_file_name ) tmp = tempfile.NamedTemporaryFile( dir=tmp_dir ).name tmp_stderr = open( tmp, 'wb' ) proc = subprocess.Popen( args=command, shell=True, cwd=tmp_dir, stderr=tmp_stderr.fileno() ) --- a/tools/samtools/bam_to_sam.xml Mon Apr 18 16:42:12 2011 -0400 +++ b/tools/samtools/bam_to_sam.xml Mon Apr 18 16:43:35 2011 -0400 @@ -1,4 +1,4 @@ -<tool id="bam_to_sam" name="BAM-to-SAM" version="1.0.1"> +<tool id="bam_to_sam" name="BAM-to-SAM" version="1.0.2"><requirements><requirement type="package">samtools</requirement></requirements> @@ -7,9 +7,11 @@ bam_to_sam.py --input1=$input1 --output1=$output1 + $header </command><inputs><param name="input1" type="data" format="bam" label="BAM File to Convert" /> + <param name="header" type="boolean" truevalue="--header" falsevalue="" checked="False" label="Include header in output" /></inputs><outputs><data format="sam" name="output1" label="${tool.name} on ${on_string}: converted SAM" /> @@ -22,6 +24,7 @@ --><param name="input1" value="1.bam" ftype="bam" /><output name="output1" file="bam_to_sam_out1.sam" sorted="True" /> + <param name="header" value="" /></test><test><!-- @@ -30,6 +33,16 @@ --><param name="input1" value="3unsorted.bam" ftype="bam" /><output name="output1" file="bam_to_sam_out2.sam" sorted="True" /> + <param name="header" value="" /> + </test> + <test> + <!-- + Bam-to-Sam command: + samtools view -h -o bam_to_sam_out1.sam test-data/1.bam + --> + <param name="input1" value="1.bam" ftype="bam" /> + <output name="output1" file="bam_to_sam_out3.sam" sorted="True" /> + <param name="header" value="True" /></test></tests><help> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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