# HG changeset patch
# User fubar
# Date 1386206669 18000
# Node ID ef1f89257fdbe18d12f7fdb13327633adec37719
# Parent a76ecde597e1cca64cf57ce324921ca63b4e005d
Deleted selected files
diff -r a76ecde597e1 -r ef1f89257fdb weblogo3-91fa0a8ce39d/rgweblogo/README
--- a/weblogo3-91fa0a8ce39d/rgweblogo/README Wed Dec 04 19:58:06 2013 -0500
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,38 +0,0 @@
-This is a Galaxy tool wrapper for weblogo3 already available as a web app at the site below but neat as a Galaxy tool
-Last updated by Ross to install iuc ghostscript and numpy dependencies.
-
-Weblogo generates sequence logos from fasta files such as the alignments generated by clustalw
-
-Note that the image for the help must be in static/images for it to show up on the tool form - it's the same image as goes in test-data
-
-**Automated Installation**
-As a Galaxy admin, use the admin menu and select the search ToolShed option. This tool should be on the main toolshed - if not try the test toolshed.
-Select it and choose "preview and install" - the process of downloading and installing weblogo3.3 and this wrapper should take a few minutes at most.
-
-** Manual Installation**
-
-Don't.
-
-If you insist,
-Make sure weblogo3 is installed in your system python and is available on the path for all your nodes
-
-Move the test data files to your galaxy root test-data
-Move the xml file to a subdirectory of your tools folder (eg rgenetics/) and then add a line in your tool_conf.xml to point there.
-Run
-sh run_functional_tests.sh -id weblogo3
-to make sure the tests work
-
-then restart Galaxy and you should be good to go.
-
-
-**Attribution**
-
-Source for the weblogo3 python executable is at http://weblogo.berkeley.edu
-
-Galaxy tool wrapper written by Ross Lazarus for the Rgenetics project
-
-Copyright Ross Lazarus at gmail com 2011
-
-All rights reserved.
-
-Released under the LGPL - see http://www.gnu.org/copyleft/lesser.html
diff -r a76ecde597e1 -r ef1f89257fdb weblogo3-91fa0a8ce39d/rgweblogo/rgWebLogo3.py
--- a/weblogo3-91fa0a8ce39d/rgweblogo/rgWebLogo3.py Wed Dec 04 19:58:06 2013 -0500
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,157 +0,0 @@
-"""
-# modified june 2 ross lazarus to add units option at Assaf Gordon's suggestion
-# rgWebLogo3.py
-# wrapper to check that all fasta files are same length
-
-"""
-import optparse, os, sys, subprocess, tempfile
-
-WEBLOGO = 'weblogo' # executable name for weblogo3 - confusing isn't it?
-
-class WL3:
- """
- simple wrapper class to check fasta sequence lengths are all identical
- """
- FASTASTARTSYM = '>'
- badseq = '## error - sequences in file %s are not all the same length - cannot proceed. Please read the tool documentation carefully'
-
- def __init__(self,opts=None):
- assert opts<>None,'WL3 class needs opts passed in - got None'
- self.opts = opts
- self.fastaf = file(self.opts.input,'r')
- self.clparams = {}
-
- def whereis(self,program):
- for path in os.environ.get('PATH', '').split(':'):
- if os.path.exists(os.path.join(path, program)) and not os.path.isdir(os.path.join(path, program)):
- return os.path.join(path, program)
- return None
-
- def runCL(self):
- """ construct and run a command line
- """
- wl = self.whereis(WEBLOGO)
- if not wl:
- print >> sys.stderr, '## rgWebLogo3.py error - cannot locate the weblogo binary %s on the current path' % WEBLOGO
- print >> sys.stderr, '## Please ensure it is installed and working from http://code.google.com/p/weblogo'
- sys.exit(1)
- cll = [WEBLOGO,]
- cll += [' '.join(it) for it in list(self.clparams.items())]
- cl = ' '.join(cll)
- assert cl > '', 'runCL needs a command line as clparms'
- fd,templog = tempfile.mkstemp(suffix='rgtempRun.txt')
- tlf = open(templog,'w')
- process = subprocess.Popen(cl, shell=True, stderr=tlf, stdout=tlf)
- rval = process.wait()
- tlf.close()
- tlogs = ''.join(open(templog,'r').readlines())
- if len(tlogs) > 1:
- s = '## executing %s returned status %d and log (stdout/stderr) records: \n%s\n' % (cl,rval,tlogs)
- else:
- s = '## executing %s returned status %d. Nothing appeared on stderr/stdout\n' % (cl,rval)
- os.unlink(templog) # always
- if rval <> 0:
- print >> sys.stderr, '## rgWebLogo3.py error - executing %s returned error code %d' % (cl,rval)
- print >> sys.stderr, '## This may be a data problem or a tool dependency (%s) installation problem' % WEBLOGO
- print >> sys.stderr, '## Please ensure %s is correctly installed and working on the command line -see http://code.google.com/p/weblogo' % WEBLOGO
- sys.exit(1)
- return s
-
-
- def iter_fasta(self):
- """
- generator for fasta sequences from a file
- """
- aseq = []
- seqname = None
- for i,row in enumerate(self.fastaf):
- if row.startswith(self.FASTASTARTSYM):
- if seqname <> None: # already in a sequence
- s = ''.join(aseq)
- l = len(s)
- yield (seqname,l)
- seqname = row[1:].strip()
- aseq = []
- else:
- if i > 0:
- print >> sys.stderr,'Invalid fasta file %s - does not start with %s - please read the tool documentation carefully' % (self.opts.input,self.FASTASTARTSYM)
- sys.exit(1)
- else:
- seqname = row[1:].strip()
- else: # sequence row
- if seqname == None:
- print >> sys.stderr,'Invalid fasta file %s - does not start with %s - please read the tool documentation carefully' % (self.opts.input,self.FASTASTARTSYM)
- sys.exit(1)
- else:
- aseq.append(row.strip())
-
- if seqname <> None: # last one
- l = len(''.join(aseq))
- yield (seqname,l)
-
-
- def fcheck(self):
- """ are all fasta sequence same length?
- might be mongo big
- """
- flen = None
- lasti = None
- f = self.iter_fasta()
- for i,(seqname,seqlen) in enumerate(f):
- lasti = i
- if i == 0:
- flen = seqlen
- else:
- if seqlen <> flen:
- print >> sys.stderr,self.badseq % self.opts.input
- sys.exit(1)
- return '# weblogo input %s has %d sequences all of length %d' % (self.opts.input,lasti,flen)
-
-
- def run(self):
- check = self.fcheck()
- self.clparams['-f'] = self.opts.input
- self.clparams['-o'] = self.opts.output
- self.clparams['-t'] = '"%s"' % self.opts.logoname # must be wrapped as a string
- self.clparams['-F'] = self.opts.outformat
- if self.opts.size <> None:
- self.clparams['-s'] = self.opts.size
- if self.opts.lower <> None:
- self.clparams['-l'] = self.opts.lower
- if self.opts.upper <> None:
- self.clparams['-u'] = self.opts.upper
- if self.opts.colours <> None:
- self.clparams['-c'] = self.opts.colours
- if self.opts.units <> None:
- self.clparams['-U'] = self.opts.units
- s = self.runCL()
- return check,s
-
-
-if __name__ == '__main__':
- '''
- called as
-
- rgWebLogo3.py --outformat $outformat -s $size -i $input -o $output -t "$logoname" -c "$colours"
-#if $range.mode == 'part'
--l "$range.seqstart" -u "$range.seqend"
-#end if
-
-
- '''
- op = optparse.OptionParser()
- op.add_option('-i', '--input', default=None)
- op.add_option('-F', '--outformat', default='png')
- op.add_option('-s', '--size', default=None)
- op.add_option('-o', '--output', default='rgWebLogo3')
- op.add_option('-t', '--logoname', default='rgWebLogo3')
- op.add_option('-c', '--colours', default=None)
- op.add_option('-l', '--lower', default=None)
- op.add_option('-u', '--upper', default=None)
- op.add_option('-U', '--units', default=None)
- opts, args = op.parse_args()
- assert opts.input <> None,'weblogo3 needs a -i parameter with a fasta input file - cannot open'
- assert os.path.isfile(opts.input),'weblogo3 needs a valid fasta input file - cannot open %s' % opts.input
- w = WL3(opts)
- checks,s = w.run()
- print >> sys.stdout, checks # for info
diff -r a76ecde597e1 -r ef1f89257fdb weblogo3-91fa0a8ce39d/rgweblogo/rgWebLogo3.xml
--- a/weblogo3-91fa0a8ce39d/rgweblogo/rgWebLogo3.xml Wed Dec 04 19:58:06 2013 -0500
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,145 +0,0 @@
-
-
-
-
-
- package_weblogo
- numpy
- ghostscript
-
- Generator from fasta
-
- rgWebLogo3.py -F $outformat -s $size -i $input -o $output -t "$logoname" -c "$colours" -U "$units"
-#if $range.mode == 'part'
--l "$range.seqstart" -u "$range.seqend"
-#end if
-
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-
-**Note**
-
-This tool uses Weblogo3_ in Galaxy to generate a sequence logo. The input file must be a fasta file in your current history.
-
-It is recommended for (eg) viewing multiple sequence alignments output from the clustalw tool - set the output to fasta and feed
-it in to this tool.
-
-A typical output looks like this
-
-.. image:: $PATH_TO_IMAGES/rgWebLogo3_test.jpg
-
-----
-
-**Warning about input Fasta format files**
-
-The Weblogo3 program used by this tool will fail if your fasta sequences are not all EXACTLY the same length. The tool will provide a warning
-and refuse to call the weblogo3 executable if irregular length sequences are detected.
-
-Fasta alignments from the companion ClustalW Galaxy tool will work but many other fasta files may cause this tool to fail - please do not file
-a Galaxy bug report - this is a feature of the tool and a problem with your source data - not a tool error - please make certain all your fasta
-sequences are exactly the same length!
-
-
-**Attribution**
-
-Weblogo attribution and associated documentation are available at Weblogo3_
-
-This Galaxy wrapper calls their software so depends on it and their license for your legal comfort.
-The wrapper was written by Ross Lazarus for the rgenetics project and the source code is licensed under the LGPL_ like other rgenetics artefacts
-
-.. _Weblogo3: http://weblogo.threeplusone.com/manual.html
-
-.. _LGPL: http://www.gnu.org/copyleft/lesser.html
-
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diff -r a76ecde597e1 -r ef1f89257fdb weblogo3-91fa0a8ce39d/rgweblogo/test-data/rgClustal_testout.fasta
--- a/weblogo3-91fa0a8ce39d/rgweblogo/test-data/rgClustal_testout.fasta Wed Dec 04 19:58:06 2013 -0500
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,48 +0,0 @@
->c_briggsae-chrII_+_
----ATGAGCTTCCACAAAAGCATGAGCTTT
-CTCAGCTTCTGCCACATCAGCATTCAAATG
-ATC
->c_brenneri-Cbre_Contig60_+_
----ATGAGCCTCCACAACAGCATGATTTTT
-CTCGGCTTCCGCCACATCCGCATTCAAATG
-ATC
->c_remanei-Crem_Contig172_-_
----ATGAGCCTCTACAACCGCATGATTCTT
-TTCAGCCTCTGCCACGTCCGCATTCAAATG
-CTC
->c_elegans-II_+_
----ATGAGCCTCTACTACAGCATGATTCTT
-CTCAGCTTCTGCAACGTCAGCATTCAGATG
-ATC
->c_briggsae-chrII_+_bar
----CCGGAGTCGATCCCTGAAT--------
-------------------------------
----
->c_brenneri-Cbre_Contig60fee_+_
----ACGAAGTCGATCCCTGAAA--------
--TCAGATGAGCGGTTGACCA---GAGAACA
-ACC
->c_remanei-Crem_Contig172zot_-_
----ACGAAGTCGGTCCCTATAAGGTATGAT
-TTTATATGA----TGTACCATAAGGAAATA
-GTC
->c_elegans-II_+_meh
----ACGAAGTCGGTCCCTGAAC--AATTAT
-TT----TGA----TATA---GAAAGAAACG
-GTA
->c_briggsae-chrIfooI_+_
-CGCACAAATATGATGCACAAATCCACAACC
-TAAAGCATCTCCGATAACGTTGACCGAAGT
----
->c_brenneri-Cbre_Contig60gak_+_
-CGCACAAATGTAGTGGACAAATCCGCATCC
-CAAAGCGTCTCCGATAACATTTACCGAAGT
----
->c_remanei-Crem_Contig172foo_-_
-AGCACAAATGTAATGAACGAATCCGCATCC
-CAACGCATCGCCAATCACATTCACAGATGT
----
->c_elegans-II_+_more
-TGCACAAATGTGATGAACGAATCCACATCC
-CAATGCATCACCGATCACATTGACAGATGT
----
diff -r a76ecde597e1 -r ef1f89257fdb weblogo3-91fa0a8ce39d/rgweblogo/test-data/rgWebLogo3_test.jpg
Binary file weblogo3-91fa0a8ce39d/rgweblogo/test-data/rgWebLogo3_test.jpg has changed
diff -r a76ecde597e1 -r ef1f89257fdb weblogo3-91fa0a8ce39d/rgweblogo/test-data/rgWebLogo3_test2.png
Binary file weblogo3-91fa0a8ce39d/rgweblogo/test-data/rgWebLogo3_test2.png has changed
diff -r a76ecde597e1 -r ef1f89257fdb weblogo3-91fa0a8ce39d/rgweblogo/tool_dependencies.xml
--- a/weblogo3-91fa0a8ce39d/rgweblogo/tool_dependencies.xml Wed Dec 04 19:58:06 2013 -0500
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,43 +0,0 @@
-
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- http://weblogo.googlecode.com/files/weblogo-3.3.tar.gz
- echo `ls -lt` && echo `pwd`
-
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- $INSTALL_DIR/lib/python
- export PYTHONPATH=$INSTALL_DIR/lib/python:$PYTHONPATH_NUMPY:$PYTHONPATH &&
- python setup.py install --home $INSTALL_DIR --install-scripts $INSTALL_DIR/bin
-
- $INSTALL_DIR/lib/python
- $ENV[PYTHONPATH_NUMPY]
- $ENV[PATH_NUMPY]
- $INSTALL_DIR/bin
- $INSTALL_DIR/bin/weblogo
-
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- weblogo3 is a python version of the old weblogo2.8 or so. Requires numpy and ghostscript so these are installed if not already on your system - if that happens, please be patient
- while numpy compiles - especially if the ATLAS libraries are being installed - which is not at present.
-
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-