1 new commit in galaxy-central:

https://bitbucket.org/galaxy/galaxy-central/commits/34b03e0f3182/ Changeset: 34b03e0f3182 User: fubar Date: 2013-05-30 06:57:13 Summary: Starting the Rgenetics deprecation process - removing all rgenetics sections from tool_conf.xml.sample and fastqc update to dance around EBI_SRA download bogus file extensions Affected #: 3 files

diff -r cc25fdb717ebde12121948a318bb9d141eb6710a -r 34b03e0f3182af0601d747b7988308ddc2931149 tool_conf.xml.sample --- a/tool_conf.xml.sample +++ b/tool_conf.xml.sample @@ -397,38 +397,6 @@ <section name="NGS: Simulation" id="ngs-simulation"><tool file="ngs_simulation/ngs_simulation.xml" /></section> - <section name="SNP/WGA: Data; Filters" id="rgdat"> - - <label text="Data: Import and upload" id="rgimport" /> - <tool file="data_source/upload.xml"/> - <tool file="data_source/access_libraries.xml" /> - - <label text="Data: Filter and Clean" id="rgfilter" /> - <tool file="rgenetics/rgClean.xml"/> - <tool file="rgenetics/rgPedSub.xml"/> - <tool file="rgenetics/rgLDIndep.xml"/> - - <label text="Simulate" id="rgsim" /> - <tool file="rgenetics/rgfakePhe.xml"/> - <tool file="rgenetics/rgfakePed.xml"/> - </section> - <section name="SNP/WGA: QC; LD; Plots" id="rgqcplot"> - - <label text="QC; Eigenstrat" id="rgvisual" /> - <tool file="rgenetics/rgQC.xml"/> - <tool file="rgenetics/rgEigPCA.xml"/> - - <label text="LD; Manhattan/QQ; GRR" id="rgld" /> - <tool file="rgenetics/rgHaploView.xml"/> - <tool file="rgenetics/rgManQQ.xml"/> - <tool file="rgenetics/rgGRR.xml"/> - </section> - <section name="SNP/WGA: Statistical Models" id="rgmodel"> - <tool file="rgenetics/rgCaCo.xml"/> - <tool file="rgenetics/rgTDT.xml"/> - <tool file="rgenetics/rgGLM.xml"/> - <tool file="rgenetics/rgManQQ.xml"/> - </section><section name="Phenotype Association" id="hgv"><tool file="evolution/codingSnps.xml" /><tool file="evolution/add_scores.xml" />

diff -r cc25fdb717ebde12121948a318bb9d141eb6710a -r 34b03e0f3182af0601d747b7988308ddc2931149 tools/rgenetics/rgFastQC.py --- a/tools/rgenetics/rgFastQC.py +++ b/tools/rgenetics/rgFastQC.py @@ -1,4 +1,5 @@ """ +# May 2013 ross added check for bogus gz extension - fastqc gets confused # added sanitizer for user supplied name # removed shell and make cl a sequence for Popen call # ross lazarus August 10 2012 in response to anon insecurity report @@ -24,6 +25,8 @@ import shutil import tempfile from rgutils import getFileString +import zipfile +import gzip

class FastQC(): """wrapper @@ -56,7 +59,32 @@ cl.append('--contaminants=%s' % self.opts.contaminants) # patch suggested by bwlang https://bitbucket.org/galaxy/galaxy-central/pull-request/30 # use a symlink in a temporary directory so that the FastQC report reflects the history input file name - fastqinfilename = re.sub(ur'[^a-zA-Z0-9_-.]', '_', os.path.basename(self.opts.inputfilename)) + infname = self.opts.inputfilename + linf = infname.lower() + trimext = False + isgz = linf.endswith('.gz') or linf.endswith('.gzip') + # decompression at upload currently does NOT remove this now bogus ending - fastqc will barf + # patched may 29 2013 until this is fixed properly + if isgz: + f = gzip.open(self.opts.input) + try: + testrow = f.readline() + except: + trimext = True + f.close() + elif linf.endswith('bz2'): + f = bz2.open(self.opts.input,'rb') + try: + f.readline() + except: + trimext = True + f.close() + elif linf.endswith('.zip'): + if not zipfile.is_zipfile(self.opts.input): + trimext = True + if trimext: + infname = os.path.splitext(infname)[0] + fastqinfilename = re.sub(ur'[^a-zA-Z0-9_-.]', '_', os.path.basename(infname)) link_name = os.path.join(self.opts.outputdir, fastqinfilename) os.symlink(self.opts.input, link_name) cl.append(link_name)

diff -r cc25fdb717ebde12121948a318bb9d141eb6710a -r 34b03e0f3182af0601d747b7988308ddc2931149 tools/rgenetics/rgFastQC.xml --- a/tools/rgenetics/rgFastQC.xml +++ b/tools/rgenetics/rgFastQC.xml @@ -1,4 +1,4 @@ -<tool name="FastQC:Read QC" id="fastqc" version="0.51"> +<tool name="FastQC:Read QC" id="fastqc" version="0.52"><description>reports using FastQC</description><command interpreter="python"> rgFastQC.py -i "$input_file" -d "$html_file.files_path" -o "$html_file" -n "$out_prefix" -f "$input_file.ext" -j "$input_file.name" -e "${GALAXY_DATA_INDEX_DIR}/shared/jars/FastQC/fastqc"

Repository URL: https://bitbucket.org/galaxy/galaxy-central/

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