Added version info to stdout for NGS tools

tools/ngs_rna/cuffcompare_wrapper.py

@@ -23,9 +23,27 @@ def __main__():
     parser.add_option( '', '--input2-tmap-output', dest='input2_tmap_output_file', help='' )
     parser.add_option( '', '--input2-refmap-output', dest='input2_refmap_output_file', help='' )
     
-    
     (options, args) = parser.parse_args()
     
+    # output version # of tool
+    try:
+        tmp = tempfile.NamedTemporaryFile().name
+        tmp_stdout = open( tmp, 'wb' )
+        proc = subprocess.Popen( args='cuffcompare 2>&1', shell=True, stdout=tmp_stdout )
+        tmp_stdout.close()
+        returncode = proc.wait()
+        stdout = None
+        for line in open( tmp_stdout.name, 'rb' ):
+            if line.lower().find( 'cuffcompare v' ) >= 0:
+                stdout = line.strip()
+                break
+        if stdout:
+            sys.stdout.write( '%s\n' % stdout )
+        else:
+            raise Exception
+    except:
+        sys.stdout.write( 'Could not determine Cuffcompare version\n' )
+
     # Make temp directory for output.
     tmp_output_dir = tempfile.mkdtemp()
     
@@ -104,4 +122,4 @@ def __main__():
         if not os.path.exists( tmp_output_dir ):
             shutil.rmtree( tmp_output_dir )
 
-if __name__=="__main__": __main__()
+if __name__=="__main__": __main__()

tools/ngs_rna/cuffdiff_wrapper.py

@@ -43,6 +43,25 @@ def __main__():
     
     (options, args) = parser.parse_args()
     
+    # output version # of tool
+    try:
+        tmp = tempfile.NamedTemporaryFile().name
+        tmp_stdout = open( tmp, 'wb' )
+        proc = subprocess.Popen( args='cuffdiff 2>&1', shell=True, stdout=tmp_stdout )
+        tmp_stdout.close()
+        returncode = proc.wait()
+        stdout = None
+        for line in open( tmp_stdout.name, 'rb' ):
+            if line.lower().find( 'cuffdiff v' ) >= 0:
+                stdout = line.strip()
+                break
+        if stdout:
+            sys.stdout.write( '%s\n' % stdout )
+        else:
+            raise Exception
+    except:
+        sys.stdout.write( 'Could not determine Cuffdiff version\n' )
+
     # Make temp directory for output.
     tmp_output_dir = tempfile.mkdtemp()
     
@@ -125,4 +144,4 @@ def __main__():
         if os.path.exists( tmp_output_dir ):
             shutil.rmtree( tmp_output_dir )
 
-if __name__=="__main__": __main__()
+if __name__=="__main__": __main__()

tools/ngs_rna/cufflinks_wrapper.py

@@ -32,6 +32,25 @@ def __main__():
     
     (options, args) = parser.parse_args()
     
+    # output version # of tool
+    try:
+        tmp = tempfile.NamedTemporaryFile().name
+        tmp_stdout = open( tmp, 'wb' )
+        proc = subprocess.Popen( args='cufflinks 2>&1', shell=True, stdout=tmp_stdout )
+        tmp_stdout.close()
+        returncode = proc.wait()
+        stdout = None
+        for line in open( tmp_stdout.name, 'rb' ):
+            if line.lower().find( 'cufflinks v' ) >= 0:
+                stdout = line.strip()
+                break
+        if stdout:
+            sys.stdout.write( '%s\n' % stdout )
+        else:
+            raise Exception
+    except:
+        sys.stdout.write( 'Could not determine Cufflinks version\n' )
+
     # Make temp directory for output.
     tmp_output_dir = tempfile.mkdtemp()
     
@@ -109,4 +128,4 @@ def __main__():
         if os.path.exists( tmp_output_dir ):
             shutil.rmtree( tmp_output_dir )
 
-if __name__=="__main__": __main__()
+if __name__=="__main__": __main__()

tools/ngs_rna/tophat_wrapper.py

@@ -67,6 +67,21 @@ def __main__():
 
     (options, args) = parser.parse_args()
 
+    # output version # of tool
+    try:
+        tmp = tempfile.NamedTemporaryFile().name
+        tmp_stdout = open( tmp, 'wb' )
+        proc = subprocess.Popen( args='tophat -v', shell=True, stdout=tmp_stdout )
+        tmp_stdout.close()
+        returncode = proc.wait()
+        stdout = open( tmp_stdout.name, 'rb' ).readline().strip()
+        if stdout:
+            sys.stdout.write( '%s\n' % stdout )
+        else:
+            raise Exception
+    except:
+        sys.stdout.write( 'Could not determine Tophat version\n' )
+
     # Creat bowtie index if necessary.
     tmp_index_dir = tempfile.mkdtemp()
     if options.own_file:

tools/ngs_rna/tophat_wrapper.xml

@@ -350,8 +350,8 @@
         <!-- Test using test data: paired-end reads, index from history. -->
         <test>
             <!-- TopHat commands:
-            bowtie-build -f test-data/tophat_in4.fasta tophat_in4
-            tophat -o tmp_dir -p 1 -r 20 tophat_in4 test-data/tophat_in2.fastqsanger test-data/tophat_in3.fastqsanger
+            bowtie-build -f test-data/tophat_in1.fasta tophat_in1
+            tophat -o tmp_dir -p 1 -r 20 tophat_in1 test-data/tophat_in2.fastqsanger test-data/tophat_in3.fastqsanger
             -->
             <param name="genomeSource" value="history" />
             <param name="ownFile" ftype="fasta" value="tophat_in1.fasta" />

tools/samtools/bam_to_sam.py

@@ -23,6 +23,25 @@ def __main__():
     parser.add_option( '', '--output1', dest='output1', help='The output BAM dataset' )
     ( options, args ) = parser.parse_args()
 
+    # output version # of tool
+    try:
+        tmp = tempfile.NamedTemporaryFile().name
+        tmp_stdout = open( tmp, 'wb' )
+        proc = subprocess.Popen( args='samtools 2>&1', shell=True, stdout=tmp_stdout )
+        tmp_stdout.close()
+        returncode = proc.wait()
+        stdout = None
+        for line in open( tmp_stdout.name, 'rb' ):
+            if line.lower().find( 'version' ) >= 0:
+                stdout = line.strip()
+                break
+        if stdout:
+            sys.stdout.write( 'Samtools %s\n' % stdout )
+        else:
+            raise Exception
+    except:
+        sys.stdout.write( 'Could not determine Samtools version\n' )
+
     tmp_dir = tempfile.mkdtemp()
 
     try:

tools/samtools/sam_merge.py

@@ -21,6 +21,24 @@ def __main__():
     if len( sys.argv ) < 3:
         stop_err( 'There are not enough files to merge' )
     filenames = sys.argv[3:]
+    # output version # of tool
+    try:
+        tmp = tempfile.NamedTemporaryFile().name
+        tmp_stdout = open( tmp, 'wb' )
+        proc = subprocess.Popen( args='samtools 2>&1', shell=True, stdout=tmp_stdout )
+        tmp_stdout.close()
+        returncode = proc.wait()
+        stdout = None
+        for line in open( tmp_stdout.name, 'rb' ):
+            if line.lower().find( 'version' ) >= 0:
+                stdout = line.strip()
+                break
+        if stdout:
+            sys.stdout.write( 'Samtools %s\n' % stdout )
+        else:
+            raise Exception
+    except:
+        sys.stdout.write( 'Could not determine Samtools version\n' )
     cmd = 'samtools merge %s %s %s' % ( outfile, infile, ' '.join( filenames ) )
     tmp = tempfile.NamedTemporaryFile().name
     try:

tools/samtools/sam_pileup.py

@@ -49,6 +49,24 @@ def __main__():
     #Parse Command Line
     options, args = doc_optparse.parse( __doc__ )
     seqPath = check_seq_file( options.dbkey, options.indexDir )
+    # output version # of tool
+    try:
+        tmp = tempfile.NamedTemporaryFile().name
+        tmp_stdout = open( tmp, 'wb' )
+        proc = subprocess.Popen( args='samtools 2>&1', shell=True, stdout=tmp_stdout )
+        tmp_stdout.close()
+        returncode = proc.wait()
+        stdout = None
+        for line in open( tmp_stdout.name, 'rb' ):
+            if line.lower().find( 'version' ) >= 0:
+                stdout = line.strip()
+                break
+        if stdout:
+            sys.stdout.write( 'Samtools %s\n' % stdout )
+        else:
+            raise Exception
+    except:
+        sys.stdout.write( 'Could not determine Samtools version\n' )
     #prepare file names 
     tmpDir = tempfile.mkdtemp()
     tmpf0 = tempfile.NamedTemporaryFile( dir=tmpDir )

tools/samtools/sam_to_bam.py

@@ -42,6 +42,25 @@ def __main__():
     parser.add_option( '', '--index_dir', dest='index_dir', help='GALAXY_DATA_INDEX_DIR' )
     ( options, args ) = parser.parse_args()
 
+    # output version # of tool
+    try:
+        tmp = tempfile.NamedTemporaryFile().name
+        tmp_stdout = open( tmp, 'wb' )
+        proc = subprocess.Popen( args='samtools 2>&1', shell=True, stdout=tmp_stdout )
+        tmp_stdout.close()
+        returncode = proc.wait()
+        stdout = None
+        for line in open( tmp_stdout.name, 'rb' ):
+            if line.lower().find( 'version' ) >= 0:
+                stdout = line.strip()
+                break
+        if stdout:
+            sys.stdout.write( 'Samtools %s\n' % stdout )
+        else:
+            raise Exception
+    except:
+        sys.stdout.write( 'Could not determine Samtools version\n' )
+
     cached_seqs_pointer_file = '%s/sam_fa_indices.loc' % options.index_dir
     if not os.path.exists( cached_seqs_pointer_file ):
         stop_err( 'The required file (%s) does not exist.' % cached_seqs_pointer_file )

tools/sr_mapping/PerM.xml

@@ -1,10 +1,11 @@
-<tool id="PerM" name="Map with PerM" version="1.1.0">
+<tool id="PerM" name="Map with PerM" version="1.1.1">
   <description>for SOLiD and Illumina</description>
   <!-- works with PerM version 0.2.6 -->
   <requirements>
       <requirement type="package">perm</requirement>
   </requirements>
   <command>
+    echo -n "PerM "; PerM 2>&amp;1 | grep "Version";
     PerM
       #if $s.sourceOfRef.refSource == "history"
         $s.sourceOfRef.ref

tools/sr_mapping/bfast_wrapper.py

@@ -82,6 +82,25 @@ def __main__():
     
     (options, args) = parser.parse_args()
 
+    # output version # of tool
+    try:
+        tmp = tempfile.NamedTemporaryFile().name
+        tmp_stdout = open( tmp, 'wb' )
+        proc = subprocess.Popen( args='bfast 2>&1', shell=True, stdout=tmp_stdout )
+        tmp_stdout.close()
+        returncode = proc.wait()
+        stdout = None
+        for line in open( tmp_stdout.name, 'rb' ):
+            if line.lower().find( 'version' ) >= 0:
+                stdout = line.strip()
+                break
+        if stdout:
+            sys.stdout.write( '%s\n' % stdout )
+        else:
+            raise Exception
+    except:
+        sys.stdout.write( 'Could not determine BFAST version\n' )
+
     buffsize = 1048576
 
     # make temp directory for bfast, requires trailing slash

tools/sr_mapping/bowtie_wrapper.py

@@ -123,6 +123,25 @@ def __main__():
     (options, args) = parser.parse_args()
     stdout = ''
 
+    # output version # of tool
+    try:
+        tmp = tempfile.NamedTemporaryFile().name
+        tmp_stdout = open( tmp, 'wb' )
+        proc = subprocess.Popen( args='bowtie --version', shell=True, stdout=tmp_stdout )
+        tmp_stdout.close()
+        returncode = proc.wait()
+        stdout = None
+        for line in open( tmp_stdout.name, 'rb' ):
+            if line.lower().find( 'version' ) >= 0:
+                stdout = line.strip()
+                break
+        if stdout:
+            sys.stdout.write( '%s\n' % stdout )
+        else:
+            raise Exception
+    except:
+        sys.stdout.write( 'Could not determine Bowtie version\n' )
+
     # make temp directory for placement of indices and copy reference file there if necessary
     tmp_index_dir = tempfile.mkdtemp()
     # get type of data (solid or solexa)

tools/sr_mapping/bwa_wrapper.py

@@ -72,6 +72,26 @@ def __main__():
     parser.add_option( '-X', '--do_not_build_index', dest='do_not_build_index', help="Don't build index" )
     parser.add_option( '-H', '--suppressHeader', dest='suppressHeader', help='Suppress header' )
     (options, args) = parser.parse_args()
+
+    # output version # of tool
+    try:
+        tmp = tempfile.NamedTemporaryFile().name
+        tmp_stdout = open( tmp, 'wb' )
+        proc = subprocess.Popen( args='bwa 2>&1', shell=True, stdout=tmp_stdout )
+        tmp_stdout.close()
+        returncode = proc.wait()
+        stdout = None
+        for line in open( tmp_stdout.name, 'rb' ):
+            if line.lower().find( 'version' ) >= 0:
+                stdout = line.strip()
+                break
+        if stdout:
+            sys.stdout.write( 'BWA %s\n' % stdout )
+        else:
+            raise Exception
+    except:
+        sys.stdout.write( 'Could not determine BWA version\n' )
+
     # make temp directory for placement of indices
     tmp_index_dir = tempfile.mkdtemp()
     tmp_dir = tempfile.mkdtemp()

tools/sr_mapping/lastz_paired_reads_wrapper.py

@@ -756,8 +756,27 @@ def __main__():
     parser.add_option( '', '--input4', dest='input4', help='The base quality score 454 file' )
     parser.add_option( '', '--output', dest='output', help='The output file' )
     parser.add_option( '', '--lastz_seqs_file_dir', dest='lastz_seqs_file_dir', help='Directory of local lastz_seqs.loc file' )
-
     ( options, args ) = parser.parse_args()
+
+    # output version # of tool
+    try:
+        tmp = tempfile.NamedTemporaryFile().name
+        tmp_stdout = open( tmp, 'wb' )
+        proc = subprocess.Popen( args='lastz -v', shell=True, stdout=tmp_stdout )
+        tmp_stdout.close()
+        returncode = proc.wait()
+        stdout = None
+        for line in open( tmp_stdout.name, 'rb' ):
+            if line.lower().find( 'version' ) >= 0:
+                stdout = line.strip()
+                break
+        if stdout:
+            sys.stdout.write( '%s\n' % stdout )
+        else:
+            raise Exception
+    except:
+        sys.stdout.write( 'Could not determine Lastz version\n' )
+
     if options.ref_name:
         ref_name = '[nickname=%s]' % options.ref_name
     else:

tools/sr_mapping/lastz_wrapper.py

@@ -152,6 +152,25 @@ def __main__():
     parser.add_option( '', '--lastzSeqsFileDir', dest='lastzSeqsFileDir', help='Directory of local lastz_seqs.loc file' )
     ( options, args ) = parser.parse_args()
 
+    # output version # of tool
+    try:
+        tmp = tempfile.NamedTemporaryFile().name
+        tmp_stdout = open( tmp, 'wb' )
+        proc = subprocess.Popen( args='lastz -v', shell=True, stdout=tmp_stdout )
+        tmp_stdout.close()
+        returncode = proc.wait()
+        stdout = None
+        for line in open( tmp_stdout.name, 'rb' ):
+            if line.lower().find( 'version' ) >= 0:
+                stdout = line.strip()
+                break
+        if stdout:
+            sys.stdout.write( '%s\n' % stdout )
+        else:
+            raise Exception
+    except:
+        sys.stdout.write( 'Could not determine Lastz version\n' )
+
     if options.unmask == 'yes':
         unmask = '[unmask]'
     else:

tools/sr_mapping/lastz_wrapper.xml

@@ -1,4 +1,4 @@
-<tool id="lastz_wrapper_2" name="Lastz" version="1.2.0">
+<tool id="lastz_wrapper_2" name="Lastz" version="1.2.1">
     <description> map short reads against reference sequence</description>
     <command interpreter="python">lastz_wrapper.py
       #if $seq_name.how_to_name=="yes":
@@ -146,7 +146,7 @@
             You need to point to phiX.2bit somewhere on your system. b1.fasta is located in galaxy's test-data.  You will have to replace all the pluses before the
             commands with 2 dashes, as double-dash can't appear in an XML comment.
             -->
-            <param name="input2" value="b1.fasta" ftype="fasta" dbkey="phiX" />
+            <param name="input2" value="b1.fasta" ftype="fasta" />
             <param name="ref_source" value="cached" />
             <!-- this is the backwards-compatible "unique value" for this file, not an actual path -->
             <param name="input1_2bit" value="/galaxy/data/phiX/seq/phiX.2bit" />
@@ -226,7 +226,7 @@
     </tests>
     <help>
         
-**What it does**    
+**What it does**
         
 **LASTZ** is a high performance pairwise sequence aligner derived from BLASTZ. It is written by Bob Harris in Webb Miller's laboratory at Penn State University. Special scoring sets were derived to improve runtime performance and quality. This Galaxy version of LASTZ is geared towards aligning short (Illumina/Solexa, AB/SOLiD) and medium (Roche/454) reads against a reference sequence. There is excellent, extensive documentation on LASTZ available here_.