From commits-noreply@bitbucket.org Fri May 13 08:35:13 2011 From: Bitbucket To: galaxy-commits@lists.galaxyproject.org Subject: [galaxy-commits] commit/galaxy-central: 5 new changesets Date: Fri, 13 May 2011 12:34:49 +0000 Message-ID: <20110513123449.6363.92524@bitbucket01.managed.contegix.com> MIME-Version: 1.0 Content-Type: multipart/mixed; boundary="===============4545365905428317670==" --===============4545365905428317670== Content-Type: text/plain; charset="utf-8" Content-Transfer-Encoding: quoted-printable 5 new changesets in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/7c3d155fae75/ changeset: r5552:7c3d155fae75 user: fubar date: 2011-05-12 15:56:01 summary: Picard wrapper modified to use python logging module for all log= ging affected #: 2 files (419 bytes) --- a/test-data/picard_output_alignment_summary_metrics.html Wed May 11 16:02= :06 2011 -0400 +++ b/test-data/picard_output_alignment_summary_metrics.html Thu May 12 09:56= :01 2011 -0400 @@ -6,54 +6,56 @@ - +
-Galaxy tool wrapper picard_wrapper at 09/05/2011 11:03:41
The fol= lowing output files were created (click the filename to view/download a copy)= :
+Galaxy tool CollectAlignmentSummaryMetrics run at 11/05/2011 23:16:24The following output files were created (click the filename to view/down= load a copy):
CollectAlignmentSummaryMetrics.log
CollectAlignmentSummaryMetrics.metri= cs.txt

-Picard on line resources:

    +Picard on line resources
    Picard output (transposed to = make it easier to see)
    - - - - - - - - - - - - - - - - - - += + + + + + + + + + + + + + + + + += + 
    ## net.sf.picard.metrics.StringHeader
    # net.sf.picard.analysis.CollectAlignmentSummaryMetrics MAX_INSE= RT_SIZE=3D100000 ADAPTER_SEQUENCE=3D[AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTAC= ACGACGCTCTTCCGATCT, AGATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG, AATGATACGGCGACCACCGAG= ATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACCGA= TCTCGTATGCCGTCTTCTGCTTG, AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTC= CGATCT, AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG, I= S_BISULFITE_SEQUENCED=3Dfalse] INPUT=3D/export/tmp/tmpBrCiH5/database/files/0= 00/dataset_2.dat OUTPUT=3D/udd/rerla/galaxy-central/database/job_working_dire= ctory/3/dataset_3_files/CollectAlignmentSummaryMetrics.metrics.txt REFERENCE_= SEQUENCE=3D/udd/rerla/galaxy-central/database/job_working_directory/3/dataset= _3_files/CollectAlignmentSummaryMetricsDXFFCP.fasta_fake.fasta ASSUME_SORTED= =3Dtrue TMP_DIR=3D/tmp VALIDATION_STRINGENCY=3DLENIENT IS_BISULFITE_SEQUEN= CED=3Dfalse STOP_AFTER=3D0 VERBOSITY=3DINFO QUIET=3Dfalse COMPRESSION_LEVEL= =3D5 MAX_RECORDS_IN_RAM=3D500000 CREATE_INDEX=3Dfalse CREATE_MD5_FILE=3Dfalse=
    ## net.sf.picard.metrics.StringHeader
    # Started on: Mon May 09 11:03:41 EDT 2011
    ## METRICS CLASS net.sf.picard.analysis.AlignmentSummaryMet= rics
    CATEGORYFIRST_OF_PAIR
    TOTAL_READS4
    PF_READS4
    PCT_PF_READS1
    PF_NOISE_READS0
    PF_READS_ALIGNED4
    PCT_PF_READS_ALIGNED1
    PF_HQ_ALIGNED_READS4
    PF_HQ_ALIGNED_BASES404
    PF_HQ_ALIGNED_Q20_BASES28
    PF_HQ_MEDIAN_MISMATCHES78
    PF_HQ_ERROR_RATE0.777228
    MEAN_READ_LENGTH101
    READS_ALIGNED_IN_PAIRS3
    PCT_READS_ALIGNED_IN_PAIRS0.75
    BAD_CYCLES63
    STRAND_BALANCE0.25
    PCT_CHIMERAS0
    ## net.sf.picard.metrics.StringHeader
    # net.sf.picard.analysis.CollectAlig= nmentSummaryMetrics MAX_INSERT_SIZE=3D100000 ADAPTER_SEQUENCE=3D[AATGATACGGCG= ACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCTCGTATGCCGTCTTCT= GCTTG, AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAG= AGCGGTTCAGCAGGAATGCCGAGACCGATCTCGTATGCCGTCTTCTGCTTG, AATGATACGGCGACCACCGAGATC= TACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNN= NATCTCGTATGCCGTCTTCTGCTTG, IS_BISULFITE_SEQUENCED=3Dfalse] INPUT=3D/export/tm= p/tmp1-mt_l/database/files/000/dataset_2.dat OUTPUT=3D/udd/rerla/galaxy-centr= al/database/job_working_directory/3/dataset_3_files/CollectAlignmentSummaryMe= trics.metrics.txt REFERENCE_SEQUENCE=3D/udd/rerla/galaxy-central/database/job= _working_directory/3/dataset_3_files/CollectAlignmentSummaryMetricsZJS8q6.fas= ta_fake.fasta ASSUME_SORTED=3Dtrue TMP_DIR=3D/tmp VALIDATION_STRINGENCY=3DLEN= IENT IS_BISULFITE_SEQUENCED=3Dfalse STOP_AFTER=3D0 VERBOSITY=3DINFO QUIET= =3Dfalse COMPRESSION_LEVEL=3D5 MAX_RECORDS_IN_RAM=3D500000 CREATE_INDEX=3Dfal= se CREATE_MD5_FILE=3Dfalse
    ## net= .sf.picard.metrics.StringHeader
    #= Started on: Wed May 11 23:16:24 EDT 2011
    ## METRICS CLASS net.sf.picard.analysis.AlignmentSummaryMetrics
    CATEGORYFIRST_OF_PAIR 
    TOTAL_READS4 
    PF_READS4 
    PCT_PF_READS1 
    PF_NOISE_READS0 
    PF_READS_ALIGNED4 
    PCT_PF_READS_ALIGNED1 
    PF_HQ_ALIGNED_READS4 
    PF_HQ_ALIGNED_BASES404 
    PF_HQ_ALIGNED_Q20_BASES28 
    PF_HQ_MEDIAN_MISMATCHES78 
    PF_HQ_ERROR_RATE0.777228 
    MEAN_READ_LENGTH101 
    READS_ALIGNED_IN_PAIRS3 
    PCT_READS_ALIGNED_IN_PAIRS0.75 
    BAD_CYCLES63 
    STRAND_BALANCE0.25 
    PCT_CHIMERAS0 
    PCT_ADAPTER 0 -
    -Picard log
    -
    ## executing java -Xmx2g -jar /udd/rerla/galaxy-central/tool-data/share=
d/jars/CreateSequenceDictionary.jar REFERENCE=3D/tmp/CollectAlignmentSummaryM=
etricsDXFFCP.fasta OUTPUT=3D/tmp/CollectAlignmentSummaryMetricsDXFFCP.dict UR=
I=3Ddataset_1.dat TRUNCATE_NAMES_AT_WHITESPACE=3DNone returned status 0 and s=
tderr:=20
-[Mon May 09 11:03:40 EDT 2011] net.sf.picard.sam.CreateSequenceDictionary RE=
FERENCE=3D/tmp/CollectAlignmentSummaryMetricsDXFFCP.fasta OUTPUT=3D/tmp/Colle=
ctAlignmentSummaryMetricsDXFFCP.dict URI=3Ddataset_1.dat TRUNCATE_NAMES_AT_WH=
ITESPACE=3Dfalse    NUM_SEQUENCES=3D2147483647 TMP_DIR=3D/tmp/rerla VERBOSITY=
=3DINFO QUIET=3Dfalse VALIDATION_STRINGENCY=3DSTRICT COMPRESSION_LEVEL=3D5 MA=
X_RECORDS_IN_RAM=3D500000 CREATE_INDEX=3Dfalse CREATE_MD5_FILE=3Dfalse
-[Mon May 09 11:03:40 EDT 2011] net.sf.picard.sam.CreateSequenceDictionary do=
ne.
+Picard Tool Run Log
    
+
    Wed, 11 May 2011 23:16:24 INFO
+ ## executing java -Xmx2g -jar /udd/rerla/galaxy-central/tool-data/shared/ja=
rs/CreateSequenceDictionary.jar REFERENCE=3D/tmp/CollectAlignmentSummaryMetri=
csZJS8q6.fasta OUTPUT=3D/tmp/CollectAlignmentSummaryMetricsZJS8q6.dict URI=3D=
dataset_1.dat TRUNCATE_NAMES_AT_WHITESPACE=3DNone returned status 0 and stder=
r:=20
+[Wed May 11 23:16:24 EDT 2011] net.sf.picard.sam.CreateSequenceDictionary RE=
FERENCE=3D/tmp/CollectAlignmentSummaryMetricsZJS8q6.fasta OUTPUT=3D/tmp/Colle=
ctAlignmentSummaryMetricsZJS8q6.dict URI=3Ddataset_1.dat TRUNCATE_NAMES_AT_WH=
ITESPACE=3Dfalse    NUM_SEQUENCES=3D2147483647 TMP_DIR=3D/tmp/rerla VERBOSITY=
=3DINFO QUIET=3Dfalse VALIDATION_STRINGENCY=3DSTRICT COMPRESSION_LEVEL=3D5 MA=
X_RECORDS_IN_RAM=3D500000 CREATE_INDEX=3Dfalse CREATE_MD5_FILE=3Dfalse
+[Wed May 11 23:16:24 EDT 2011] net.sf.picard.sam.CreateSequenceDictionary do=
ne.
 Runtime.totalMemory()=3D9109504
=20
=20
-## executing java -Xmx2g -jar /udd/rerla/galaxy-central/tool-data/shared/jar=
s/CollectAlignmentSummaryMetrics.jar VALIDATION_STRINGENCY=3DLENIENT ASSUME_S=
ORTED=3Dtrue  ADAPTER_SEQUENCE=3D IS_BISULFITE_SEQUENCED=3Dfalse MAX_INSERT_S=
IZE=3D100000 OUTPUT=3D/udd/rerla/galaxy-central/database/job_working_director=
y/3/dataset_3_files/CollectAlignmentSummaryMetrics.metrics.txt R=3D/udd/rerla=
/galaxy-central/database/job_working_directory/3/dataset_3_files/CollectAlign=
mentSummaryMetricsDXFFCP.fasta_fake.fasta TMP_DIR=3D/tmp INPUT=3D/export/tmp/=
tmpBrCiH5/database/files/000/dataset_2.dat returned status 0 and stderr:=20
-[Mon May 09 11:03:41 EDT 2011] net.sf.picard.analysis.CollectAlignmentSummar=
yMetrics MAX_INSERT_SIZE=3D100000 ADAPTER_SEQUENCE=3D[AATGATACGGCGACCACCGAGAT=
CTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG, AATG=
ATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCGGTTCAGC=
AGGAATGCCGAGACCGATCTCGTATGCCGTCTTCTGCTTG, AATGATACGGCGACCACCGAGATCTACACTCTTTC=
CCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNNNATCTCGTATG=
CCGTCTTCTGCTTG, IS_BISULFITE_SEQUENCED=3Dfalse] INPUT=3D/export/tmp/tmpBrCiH5=
/database/files/000/dataset_2.dat OUTPUT=3D/udd/rerla/galaxy-central/database=
/job_working_directory/3/dataset_3_files/CollectAlignmentSummaryMetrics.metri=
cs.txt REFERENCE_SEQUENCE=3D/udd/rerla/galaxy-central/database/job_working_di=
rectory/3/dataset_3_files/CollectAlignmentSummaryMetricsDXFFCP.fasta_fake.fas=
ta ASSUME_SORTED=3Dtrue TMP_DIR=3D/tmp VALIDATION_STRINGENCY=3DLENIENT    IS_=
BISULFITE_SEQUENCED=3Dfalse STOP_AFTER=3D0 VERBOSITY=3DINFO QUIET=3Dfalse COM=
PRESSION_LEVEL=3D5 MAX_RECORDS_IN_RAM=3D500000 CREATE_INDEX=3Dfalse CREATE_MD=
5_FILE=3Dfalse
-WARNING	2011-05-09 11:03:41	SinglePassSamProgram	File reports sort order 'qu=
eryname', assuming it's coordinate sorted anyway.
-[Mon May 09 11:03:41 EDT 2011] net.sf.picard.analysis.CollectAlignmentSummar=
yMetrics done.
+Wed, 11 May 2011 23:16:24 INFO
+ ## executing java -Xmx2g -jar /udd/rerla/galaxy-central/tool-data/shared/ja=
rs/CollectAlignmentSummaryMetrics.jar VALIDATION_STRINGENCY=3DLENIENT ASSUME_=
SORTED=3Dtrue  ADAPTER_SEQUENCE=3D IS_BISULFITE_SEQUENCED=3Dfalse MAX_INSERT_=
SIZE=3D100000 OUTPUT=3D/udd/rerla/galaxy-central/database/job_working_directo=
ry/3/dataset_3_files/CollectAlignmentSummaryMetrics.metrics.txt R=3D/udd/rerl=
a/galaxy-central/database/job_working_directory/3/dataset_3_files/CollectAlig=
nmentSummaryMetricsZJS8q6.fasta_fake.fasta TMP_DIR=3D/tmp INPUT=3D/export/tmp=
/tmp1-mt_l/database/files/000/dataset_2.dat returned status 0 and stderr:=20
+[Wed May 11 23:16:24 EDT 2011] net.sf.picard.analysis.CollectAlignmentSummar=
yMetrics MAX_INSERT_SIZE=3D100000 ADAPTER_SEQUENCE=3D[AATGATACGGCGACCACCGAGAT=
CTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG, AATG=
ATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCGGTTCAGC=
AGGAATGCCGAGACCGATCTCGTATGCCGTCTTCTGCTTG, AATGATACGGCGACCACCGAGATCTACACTCTTTC=
CCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNNNATCTCGTATG=
CCGTCTTCTGCTTG, IS_BISULFITE_SEQUENCED=3Dfalse] INPUT=3D/export/tmp/tmp1-mt_l=
/database/files/000/dataset_2.dat OUTPUT=3D/udd/rerla/galaxy-central/database=
/job_working_directory/3/dataset_3_files/CollectAlignmentSummaryMetrics.metri=
cs.txt REFERENCE_SEQUENCE=3D/udd/rerla/galaxy-central/database/job_working_di=
rectory/3/dataset_3_files/CollectAlignmentSummaryMetricsZJS8q6.fasta_fake.fas=
ta ASSUME_SORTED=3Dtrue TMP_DIR=3D/tmp VALIDATION_STRINGENCY=3DLENIENT    IS_=
BISULFITE_SEQUENCED=3Dfalse STOP_AFTER=3D0 VERBOSITY=3DINFO QUIET=3Dfalse COM=
PRESSION_LEVEL=3D5 MAX_RECORDS_IN_RAM=3D500000 CREATE_INDEX=3Dfalse CREATE_MD=
5_FILE=3Dfalse
+WARNING	2011-05-11 23:16:24	SinglePassSamProgram	File reports sort order 'qu=
eryname', assuming it's coordinate sorted anyway.
+[Wed May 11 23:16:24 EDT 2011] net.sf.picard.analysis.CollectAlignmentSummar=
yMetrics done.
 Runtime.totalMemory()=3D9109504
=20
=20


--- a/tools/picard/picard_wrapper.py	Wed May 11 16:02:06 2011 -0400
+++ b/tools/picard/picard_wrapper.py	Thu May 12 09:56:01 2011 -0400
@@ -8,7 +8,7 @@
 see http://www.gnu.org/copyleft/lesser.html
 """
=20
-import optparse, os, sys, subprocess, tempfile, shutil, time
+import optparse, os, sys, subprocess, tempfile, shutil, time, logging
=20
 galhtmlprefix =3D """
@@ -22,7 +22,7 @@
 
    
 """
-galhtmlattr =3D """Galaxy tool wrapper %s at %s
    """
+galhtmlattr =3D """Galaxy tool %s run at %s
    """
 galhtmlpostfix =3D """
    \n"""
=20
=20
@@ -68,12 +68,24 @@
             os.makedirs(opts.tmpdir)
         except:
             pass
-        self.log_filename =3D os.path.join(opts.outdir,'%s.log' % self.picna=
me)
+        self.log_filename =3D os.path.join(self.opts.outdir,'%s.log' % self.=
picname)
         self.metricsOut =3D  os.path.join(opts.outdir,'%s.metrics.txt' % sel=
f.picname)
+        self.setLogging(logfname=3Dself.log_filename)
 =20
     def baseName(self,name=3DNone):
         return os.path.splitext(os.path.basename(name))[0]
=20
+    def setLogging(self,logfname=3D"picard_wrapper.log"):
+        """setup a logger
+        """
+        today=3Dtimenow()
+        logging.basicConfig(level=3Dlogging.INFO,
+                    format=3D'%(asctime)s %(levelname)s\n %(message)s',
+                    datefmt=3D'%a, %d %b %Y %H:%M:%S',
+                    filename=3Dlogfname,
+                    filemode=3D'a')
+
+
     def readLarge(self,fname=3DNone):
         """ read a potentially huge file..
         """
@@ -120,6 +132,7 @@
             s =3D '## executing %s returned status %d and stderr: \n%s\n' % =
(cl,rval,stderrs)
         else:
             s =3D '## executing %s returned status %d and nothing on stderr\=
n' % (cl,rval)
+        logging.info(s)
         os.unlink(templog) # always
         os.unlink(temperr) # always
         return s, stdouts # sometimes this is an output
@@ -132,10 +145,6 @@
         runme.append('-jar %s' % jar)
         runme +=3D cl
         s,stdout =3D self.runCL(cl=3Drunme, output_dir=3Dself.opts.outdir)
-        lf =3D open(self.log_filename,'a')
-        lf.write(s)
-        lf.write('\n')
-        lf.close()
         return stdout
=20
     def samToBam(self,infile=3DNone,outdir=3DNone):
@@ -180,7 +189,7 @@
         except:
             r =3D []       =20
         if len(r) > 0:
-            res.append('Picard on line resources:
      \n')
+            res.append('Picard on line resources
        \n')
             res.append('
      • Click here for Picard Documentation
        • \n')
             res.append('
      • Click here for Picard Metrics definitions
        • <=
/ul>
        \n')
             if transpose:
@@ -204,20 +213,20 @@
                         thist =3D True
                 if row.strip() =3D=3D '' or i =3D=3D lastr: # last line or b=
lank means write a segment
                     if len(heads) > 0:
-                        hres =3D ['%s' % (i =
% 2,x) for i,x in enumerate(heads)]
+                        hres =3D ['%s' % (i % 2,x) for i,x in enumerate(heads)]
                         res +=3D hres
                         heads =3D []
                     if len(dat) > 0: =20
                         if transpose and not thist:
                             tdat =3D map(None,*dat) # transpose an arbitrary=
 list of lists
-                            tdat =3D ['%s%s\n' % ((i+len(heads)) % 2,x[0],x[1]) for i,x in enumerate(tdat) if i =
< maxrows]=20
+                            tdat =3D ['%s%s&n=
bsp;\n' % ((i+len(heads)) % 2,x[0],x[1]) for i,x in enumerate(tdat)=
 if i < maxrows]=20
                             missing =3D len(tdat) - maxrows
                             if missing > 0:
                                tdat.append('...WARNING=
: %d rows deleted..see raw file %s for entire output' % (missing,os=
.path.basename(picout)))
                         else:
                             if thist or not transpose:
                                 dat =3D ['\t'.join(x).strip() for x in dat] =
# back to strings :(
-                            tdat =3D ['%s\n'=
 % ((i+len(heads)) % 2,x) for i,x in enumerate(dat) if i < maxrows]=20
+                            tdat =3D ['%=
s\n' % ((i+len(heads)) % 2,x) for i,x in enumerate(dat) if i < maxr=
ows]=20
                             missing =3D len(tdat) - maxrows
                             if missing > 0:     =20
                                 tdat.append('...WARNING: %d rows del=
eted..see raw file %s for entire output' % (missing,os.path.basenam=
e(self.metricsOut)))
@@ -231,14 +240,15 @@
         picard produces long hard to read tab header files
         make them available but present them transposed for readability
         """
+        logging.shutdown()
         self.cleanup() # remove temp files stored in delme
         rstyle=3D""""""   =20
         res =3D [rstyle,]
-        res.append(galhtmlprefix % self.picname)  =20
-        res.append(galhtmlattr % (self.progname,timenow()))
+        res.append(galhtmlprefix % self.progname)  =20
+        res.append(galhtmlattr % (self.picname,timenow()))
         flist =3D [x for x in os.listdir(self.opts.outdir) if not x.startswi=
th('.')]=20
         pdflist =3D [x for x in flist if os.path.splitext(x)[-1].lower() =3D=
=3D '.pdf']
         if len(pdflist) > 0: # assumes all pdfs come with thumbnail .jpgs
@@ -260,7 +270,7 @@
         l =3D open(self.log_filename,'r').readlines()
         llen =3D len(l)
         if llen > 0:=20
-            res.append('Picard log
        \n')=20
+            res.append('Picard Tool Run Log
        \n')=20
             rlog =3D ['
        ',]
             if llen > maxloglines:
                 rlog +=3D l[:maxloglines]               =20
@@ -295,9 +305,7 @@
         self.runCL(cl=3Dcl,output_dir=3Dself.opts.outdir)
         head =3D open(thead,'r').readlines()
         s =3D '## got %d rows of header\n' % (len(head))
-        lf =3D open(self.log_filename,'a')
-        lf.write(s)
-        lf.close()
+        logging.info(s)
         o =3D open(outf,'w')
         o.write(''.join(head))
         o.write(''.join(bed))
@@ -344,10 +352,7 @@
             infile.close()
             if newsam:
                 shutil.copy(insam,newsam)
-        lf =3D open(self.log_filename,'a')
-        lf.write(info)
-        lf.write('\n')
-        lf.close()
+        logging.info(info)
                =20
=20
=20
@@ -606,13 +611,9 @@
             s +=3D 'so please double check that your input data really is pa=
ired-end NGS data.
        \n'
             s +=3D 'If your input was paired data this may be a bug worth re=
porting to the galaxy-bugs list\n
        '
             stdouts =3D ''
-        lf =3D open(pic.log_filename,'a')
-        lf.write(s)
-        lf.write('\n')
+        logging.info(s)
         if len(stdouts) > 0:
-           lf.write(stdouts)
-           lf.write('\n')
-        lf.close()
+           logging.info(stdouts)
        =20
     elif pic.picname =3D=3D 'MarkDuplicates':
         # assume sorted even if header says otherwise


http://bitbucket.org/galaxy/galaxy-central/changeset/60ce33ea8e41/
changeset:   r5553:60ce33ea8e41
user:        fubar
date:        2011-05-12 22:48:31
summary:     update some test outputs for picard
affected #:  2 files (212 bytes)

--- a/test-data/picard_BIS_output1.txt	Thu May 12 09:56:01 2011 -0400
+++ b/test-data/picard_BIS_output1.txt	Thu May 12 16:48:31 2011 -0400
@@ -6,30 +6,31 @@
 
-
+
        
-Galaxy tool wrapper picard_wrapper at 09/05/2011 13:04:11
        The fol=
lowing output files were created (click the filename to view/download a copy)=
:
        
+Galaxy tool BamIndexStats run at 12/05/2011 14:18:06
        The followin=
g output files were created (click the filename to view/download a copy):=

        BamIndexStats.metri=
cs.txt
        BamIndexStats.log
        
-Picard on line resources:
          
+Picard on line resources
          Picard output
          
-
-
-
-
+
+
+
+
          chr1 length=3D	101	Aligned=3D 0	Unaligned=3D 0
          chr7 length=3D	404	Aligned=3D 7	Unaligned=3D 0
          chr8 length=3D	202	Aligned=3D 0	Unaligned=3D 0
          NoCoordinateCount=3D 1
          chr1 length=3D	101	Aligned=3D 0	Unaligned=
=3D 0
          chr7 length=3D	404	Aligned=3D 7	Unaligned=
=3D 0
          chr8 length=3D	202	Aligned=3D 0	Unaligned=
=3D 0
          NoCoordinateCount=3D 1
          
-Picard log
          
-
          ## executing java -Xmx2g -jar /udd/rerla/galaxy-central/tool-data/share=
d/jars/BamIndexStats.jar VALIDATION_STRINGENCY=3DLENIENT INPUT=3D/udd/rerla/g=
alaxy-central/database/job_working_directory/2/dataset_2_files/tmpMiaCgO.bam =
returned status 0 and stderr:=20
-[Mon May 09 13:04:11 EDT 2011] net.sf.picard.sam.BamIndexStats INPUT=3D/udd/=
rerla/galaxy-central/database/job_working_directory/2/dataset_2_files/tmpMiaC=
gO.bam VALIDATION_STRINGENCY=3DLENIENT    TMP_DIR=3D/tmp/rerla VERBOSITY=3DIN=
FO QUIET=3Dfalse COMPRESSION_LEVEL=3D5 MAX_RECORDS_IN_RAM=3D500000 CREATE_IND=
EX=3Dfalse CREATE_MD5_FILE=3Dfalse
-[Mon May 09 13:04:11 EDT 2011] net.sf.picard.sam.BamIndexStats done.
+Picard Tool Run Log
          
+
          Thu, 12 May 2011 14:18:06 INFO
+ ## executing java -Xmx2g -jar /udd/rerla/galaxy-central/tool-data/shared/ja=
rs/BamIndexStats.jar VALIDATION_STRINGENCY=3DLENIENT INPUT=3D/udd/rerla/galax=
y-central/database/job_working_directory/955/dataset_1015_files/tmp45bd_D.bam=
 returned status 0 and stderr:=20
+[Thu May 12 14:18:06 EDT 2011] net.sf.picard.sam.BamIndexStats INPUT=3D/udd/=
rerla/galaxy-central/database/job_working_directory/955/dataset_1015_files/tm=
p45bd_D.bam VALIDATION_STRINGENCY=3DLENIENT    TMP_DIR=3D/tmp/rerla VERBOSITY=
=3DINFO QUIET=3Dfalse COMPRESSION_LEVEL=3D5 MAX_RECORDS_IN_RAM=3D500000 CREAT=
E_INDEX=3Dfalse CREATE_MD5_FILE=3Dfalse
+[Thu May 12 14:18:06 EDT 2011] net.sf.picard.sam.BamIndexStats done.
 Runtime.totalMemory()=3D9109504
=20
=20


--- a/test-data/picard_BIS_output2.txt	Thu May 12 09:56:01 2011 -0400
+++ b/test-data/picard_BIS_output2.txt	Thu May 12 16:48:31 2011 -0400
@@ -6,32 +6,33 @@
 
-
+
          
-Galaxy tool wrapper picard_wrapper at 09/05/2011 13:04:21
          The fol=
lowing output files were created (click the filename to view/download a copy)=
:
          
+Galaxy tool BamIndexStats run at 12/05/2011 14:18:22
          The followin=
g output files were created (click the filename to view/download a copy):=

          BamIndexStats.metri=
cs.txt
          BamIndexStats.log
          
-Picard on line resources:
            
+Picard on line resources
            Picard output
            
-
-
-
-
-
-
+
+
+
+
+
+
            chr1 length=3D	101	Aligned=3D 0	Unaligned=3D 0
            chr7 length=3D	404	Aligned=3D 7	Unaligned=3D 0
            chr8 length=3D	202	Aligned=3D 0	Unaligned=3D 0
            chr10 length=3D	303	Aligned=3D 0	Unaligned=3D 0
            chr14 length=3D	505	Aligned=3D 0	Unaligned=3D 0
            NoCoordinateCount=3D 1
            chr1 length=3D	101	Aligned=3D 0	Unaligned=
=3D 0
            chr7 length=3D	404	Aligned=3D 7	Unaligned=
=3D 0
            chr8 length=3D	202	Aligned=3D 0	Unaligned=
=3D 0
            chr10 length=3D	303	Aligned=3D 0	Unaligne=
d=3D 0
            chr14 length=3D	505	Aligned=3D 0	Unaligne=
d=3D 0
            NoCoordinateCount=3D 1
            
-Picard log
            
-
            ## executing java -Xmx2g -jar /udd/rerla/galaxy-central/tool-data/share=
d/jars/BamIndexStats.jar VALIDATION_STRINGENCY=3DLENIENT INPUT=3D/udd/rerla/g=
alaxy-central/database/job_working_directory/4/dataset_4_files/tmpB_J8W5.bam =
returned status 0 and stderr:=20
-[Mon May 09 13:04:21 EDT 2011] net.sf.picard.sam.BamIndexStats INPUT=3D/udd/=
rerla/galaxy-central/database/job_working_directory/4/dataset_4_files/tmpB_J8=
W5.bam VALIDATION_STRINGENCY=3DLENIENT    TMP_DIR=3D/tmp/rerla VERBOSITY=3DIN=
FO QUIET=3Dfalse COMPRESSION_LEVEL=3D5 MAX_RECORDS_IN_RAM=3D500000 CREATE_IND=
EX=3Dfalse CREATE_MD5_FILE=3Dfalse
-[Mon May 09 13:04:21 EDT 2011] net.sf.picard.sam.BamIndexStats done.
+Picard Tool Run Log
            
+
            Thu, 12 May 2011 14:18:22 INFO
+ ## executing java -Xmx2g -jar /udd/rerla/galaxy-central/tool-data/shared/ja=
rs/BamIndexStats.jar VALIDATION_STRINGENCY=3DLENIENT INPUT=3D/udd/rerla/galax=
y-central/database/job_working_directory/957/dataset_1017_files/tmpqXGksN.bam=
 returned status 0 and stderr:=20
+[Thu May 12 14:18:21 EDT 2011] net.sf.picard.sam.BamIndexStats INPUT=3D/udd/=
rerla/galaxy-central/database/job_working_directory/957/dataset_1017_files/tm=
pqXGksN.bam VALIDATION_STRINGENCY=3DLENIENT    TMP_DIR=3D/tmp/rerla VERBOSITY=
=3DINFO QUIET=3Dfalse COMPRESSION_LEVEL=3D5 MAX_RECORDS_IN_RAM=3D500000 CREAT=
E_INDEX=3Dfalse CREATE_MD5_FILE=3Dfalse
+[Thu May 12 14:18:22 EDT 2011] net.sf.picard.sam.BamIndexStats done.
 Runtime.totalMemory()=3D9109504
=20
=20


http://bitbucket.org/galaxy/galaxy-central/changeset/c53834f418c9/
changeset:   r5554:c53834f418c9
user:        fubar
date:        2011-05-12 22:48:45
summary:     branch merge
affected #:  7 files (405 bytes)

--- a/buildbot_setup.sh	Thu May 12 16:48:31 2011 -0400
+++ b/buildbot_setup.sh	Thu May 12 16:48:45 2011 -0400
@@ -61,6 +61,7 @@
 /galaxy/data/location/srma_index.loc
 /galaxy/data/taxonomy
 /galaxy/data/location/twobit.loc
+/galaxy/software/tool-data/gatk
 "
=20
 SAMPLES=3D"
@@ -135,4 +136,7 @@
 echo "Setting up test data location files"
 python test-data-repo/location/make_location.py
=20
+echo "Appending tool-data/shared/ucsc/builds.txt.buildbot to tool-data/share=
d/ucsc/builds.txt"
+cat tool-data/shared/ucsc/builds.txt.buildbot >> tool-data/shared/ucsc/build=
s.txt
+
 python ./scripts/fetch_eggs.py all


--- a/test-data/gatk/gatk_analyze_covariates/gatk_analyze_covariates_out_1.ht=
ml	Thu May 12 16:48:31 2011 -0400
+++ b/test-data/gatk/gatk_analyze_covariates/gatk_analyze_covariates_out_1.ht=
ml	Thu May 12 16:48:45 2011 -0400
@@ -1,1 +1,17 @@
-Galaxy - GATK Output
            
\ No newline at end of file
+
+
+Galaxy - GATK Output
+
+
+
            
+
            
+
+


--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/shared/ucsc/builds.txt.buildbot	Thu May 12 16:48:45 2011 -0400
@@ -0,0 +1,1 @@
+chrM	equCab2 chrM (chrM)


--- a/tools/gatk/gatk_wrapper.py	Thu May 12 16:48:31 2011 -0400
+++ b/tools/gatk/gatk_wrapper.py	Thu May 12 16:48:45 2011 -0400
@@ -37,10 +37,10 @@
     return None
=20
 def html_report_from_directory( html_out, dir ):
-    html_out.write( 'Galaxy - GATK Output<=
body>
              ' )
-    for fname in os.listdir( dir ):
-        html_out.write(  '
            • %s
              • ' % ( fname, fname )=
 )
-    html_out.write( '
            ' )
+    html_out.write( '\n\nGalaxy - GATK Output\n\n\n
            \n
              \n' )
+    for fname in sorted( os.listdir( dir ) ):
+        html_out.write(  '
            • %s
              • \n' % ( fname, fname=
 ) )
+    html_out.write( '
            \n\n\n' )
=20
 def __main__():
     #Parse Command Line


--- a/tools/picard/picard_AddOrReplaceReadGroups.xml	Thu May 12 16:48:31 2011=
 -0400
+++ b/tools/picard/picard_AddOrReplaceReadGroups.xml	Thu May 12 16:48:45 2011=
 -0400
@@ -63,7 +63,7 @@
       
-      
+      =