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mark the example submission rule files as being raw, so the escapes dont get confused
[htsworkflow.git] / scripts /
2012-11-16 Diane TroutFurther attempts to validate RDF models. tree | commitdiff
2012-07-16 Diane TroutRemove default sequence-format so the new auto-detector... tree | commitdiff
2012-07-12 Diane Troutfix a variable name typo tree | commitdiff
2012-06-27 Diane TroutAuto-generate a secret key for django and store in... tree | commitdiff
2012-04-13 Diane TroutMerge branch 'master' of mus.cacr.caltech.edu:htsworkflow tree | commitdiff
2012-03-27 Diane TroutMerge branch 'master' of mus.cacr.caltech.edu:htsworkflow tree | commitdiff
2012-03-23 Diane TroutAdd fastq to the raw format add_xoption tree | commitdiff
2012-03-07 Diane TroutUpdate archive script to try and deal with HiSeq multip... tree | commitdiff
2012-03-07 Diane TroutUpdate help message since we have a new type of file... tree | commitdiff
2011-11-05 Diane TroutMerge branch 'master' of mus.cacr.caltech.edu:htsworkflow tree | commitdiff
2011-11-04 Diane TroutUse a logger initialized to the module name much more... tree | commitdiff
2011-10-10 Diane TroutRemove ReadPrep and Thumbnail_Images being generated... tree | commitdiff
2011-10-06 Diane TroutAdd the ability to specify a flowcell id instead of... tree | commitdiff
2011-09-17 Diane TroutAdd support for tracking the multiplex index sequence. 0.5.4 tree | commitdiff
2011-06-30 Diane TroutMerge branch 'master' of mus.cacr.caltech.edu:htsworkflow tree | commitdiff
2011-06-11 Diane TroutMerge branch 'master' of mus.cacr.caltech.edu:htsworkflow tree | commitdiff
2011-06-10 Brandon W. KingThe srf/qseq --raw-format patch. tree | commitdiff
2011-05-26 Diane TroutMerge branch 'add-condition' tree | commitdiff
2011-04-06 Diane Troutdjango-nose didn't work with django 1.1, so I went... tree | commitdiff
2011-01-25 rootMerge branch 'master' of mus.cacr.caltech.edu:htsworkflow tree | commitdiff
2011-01-21 Diane TroutMerge branch 'master' of gitosis@mus.cacr.caltech.edu... tree | commitdiff
2011-01-08 Diane TroutAdd validation script 0.5.0 tree | commitdiff
2011-01-04 Diane TroutRename all the scripts to start with htsw- tree | commitdiff
2010-10-22 Diane TroutReport version number derived from git tag. tree | commitdiff
2010-10-07 Diane TroutUpdate gerald config file generation. tree | commitdiff
2010-09-24 Diane TroutRemind myself that dry-run doesn't work with the extrac... tree | commitdiff
2010-08-24 Diane TroutBetter detect which program ids generated CNF4 srf... tree | commitdiff
2010-07-08 Diane TroutUpdate srf2named_fastq to try to detect if the srf... tree | commitdiff
2010-07-07 Diane TroutIf a quality score started with an @ sign it was treate... tree | commitdiff
2010-06-22 Diane TroutFix srf2named_fastq to output the proper /2 in paired... tree | commitdiff
2010-06-15 Diane TroutMake it easier to run srf2named_fastq.py tree | commitdiff
2010-06-15 Diane TroutWrapper script that helps convert srf files to fastq... tree | commitdiff
2010-06-10 Diane TroutMove the code to scan the sequence file archive to... tree | commitdiff
2010-06-10 Diane TroutMove the knowledge of the urls for the REST API to... tree | commitdiff
2010-05-29 Diane TroutDo not insert anything into the header if there is... tree | commitdiff
2010-05-08 Diane TroutAlways return a count from carefully_make_hardlinks tree | commitdiff
2010-04-23 Diane TroutAdd support for generating fasta files in addition... tree | commitdiff
2010-03-22 Diane TroutExtend qseq2fastq to write to two fastq files, tree | commitdiff
2010-03-05 Diane TroutUse the HTS workflow API to figure out the library... tree | commitdiff
2010-02-04 Diane TroutActually implement the code to loop over a list of... tree | commitdiff
2010-01-30 Diane TroutUpdate the inventory tracker code for the split from... tree | commitdiff
2010-01-13 Diane TroutModify qseq2fastq to also read from compressed tar... tree | commitdiff
2010-01-07 Diane TroutUpdate the usage string for qseq2fastq tree | commitdiff
2009-12-11 Diane TroutModify the srf utility to tar.bz2 the qseq files instea... tree | commitdiff
2009-12-01 Diane TroutReplace '.' with 'N' in the sequence from qseq files. tree | commitdiff
2009-12-01 Diane TroutFix typo in srf command tree | commitdiff
2009-12-01 Diane TroutAlso include the read ID in the fastq header tree | commitdiff
2009-12-01 Diane TroutAdd a simple utility to convert qseq to fastq files. tree | commitdiff
2009-10-08 Diane TroutAdd the ability not to build srf files. tree | commitdiff
2009-10-06 Diane TroutDefault to sequencing if we don't have a genome for... tree | commitdiff
2009-09-30 Diane TroutAdd building srf files to runfolder as part of --extrac... tree | commitdiff
2009-09-26 Diane TroutImplement a client side config file generator. tree | commitdiff
2009-09-16 Diane TroutReplace some prints with logging.info messages and tree | commitdiff
2009-08-12 Diane TroutConverted Brandon's scripts into a single python script... tree | commitdiff
2009-08-12 Diane TroutMove Brandon's upgrade script in with all the other... tree | commitdiff
2009-08-11 Brandon KingMaking it more clear what the script does. tree | commitdiff
2009-08-11 Brandon KingScript for conversion of db; start of fixes brought... tree | commitdiff
2009-08-10 Brandon Kingprint killing wsgi; minor fix. tree | commitdiff
2009-08-07 Brandon KingNew Lane Table migration progress. tree | commitdiff
2009-06-16 Brandon KingIcon added. tree | commitdiff
2009-06-16 Brandon KingManaged to use a urllib python 2.6 feature... convertin... tree | commitdiff
2009-06-10 Brandon KingImproved debugging output. tree | commitdiff
2009-06-10 Brandon KingMoved hardcoded URL to it's proper place in the setting... tree | commitdiff
2009-06-10 Brandon KingTrack which flowcells are archived on which long term... tree | commitdiff
2009-05-06 Diane TroutUpdate htsworkflow.util.fctracker module to work with... tree | commitdiff
2009-04-24 Diane Troutadd --clean option to runfolder tree | commitdiff
2009-04-24 Diane TroutAllow picking runfolder variant we should be trying... tree | commitdiff
2009-03-31 Diane Troutprovide an error message if no run is found with the... tree | commitdiff
2009-03-30 Diane TroutAllow specifying a run instead of just scanning the... tree | commitdiff
2009-03-30 Diane TroutAdd some logging code to report what the program is... tree | commitdiff
2009-03-28 Diane TroutFor pipeline 1.1rc1 or 1.3.2, look for the matrix files... tree | commitdiff
2009-03-18 Diane Troutprovide more options for picking how much logging info... tree | commitdiff
2009-02-27 Diane TroutOnly configure logging if we're being run as a script tree | commitdiff
2009-02-13 Diane Troutuse the compression handling auto-opener for our eland... tree | commitdiff
2009-01-30 Diane Troutextended command line configuration parsing and add... tree | commitdiff
2009-01-30 Diane TroutTry to make runfolder results extraction more robust tree | commitdiff
2009-01-24 Diane Troutinsert code to do ~ home directory expansion tree | commitdiff
2008-12-22 Diane Troutupdate make-tree-library script with new default location tree | commitdiff
2008-12-22 Diane Troutclean up the logic for deciding the output filename... tree | commitdiff
2008-12-03 Diane Troutmake-library-tree is a tool to maintain caltech's versi... tree | commitdiff
2008-11-21 Diane TroutUse the get_runs from htsworkflow.pipelines.runfolder tree | commitdiff
2008-10-30 Diane TroutThe htsworkflow.pipelines.gerald module was getting... tree | commitdiff
2008-10-21 Diane Troutupdate scripts for the pipeline to pipelines module... tree | commitdiff
2008-10-15 Diane TroutRename trunk from gaworkflow to htsworkflow (and update... tree | commitdiff
2008-09-25 Diane Troutuse _ for field seperator in srf file names. (Using... tree | commitdiff
2008-09-18 Diane TroutUse queuecommands.run not queuecommands.start_job to... tree | commitdiff
2008-08-29 Diane TroutAdd support for converting mutli-eland files from pipel... tree | commitdiff
2008-08-15 Diane TroutImprove code to extract runfolder name from the path... tree | commitdiff
2008-08-14 Diane TroutUtility to create srf files from a bustard directory tree | commitdiff
2008-08-11 Diane TroutA bit of refactoring toward making the run progress... tree | commitdiff
2008-06-05 Diane Troutadd --extract-results to scripts/runfolder tree | commitdiff
2008-05-28 Diane TroutCompute all the details needed to create our 25bp rerun... tree | commitdiff
2008-05-23 Diane Troutadd --run-xml to runfolder so you can generate summary... tree | commitdiff
2008-05-15 Diane Troutadd rerun_eland.py which extracts sub-sequences from... tree | commitdiff
2008-05-13 Diane Troutlogging.basicConfig should only be in top level scripts. tree | commitdiff
2008-05-09 Diane TroutMove runfolder analysis classes out of scripts/runfolde... tree | commitdiff
2008-04-24 Diane TroutAdd a script that takes a set of eland_result files... tree | commitdiff
2008-04-24 Diane TroutReport cluster results with the rest of the lane summar... tree | commitdiff
2008-04-22 Diane Troutoops forgot to remove some debugging statements from... tree | commitdiff
2008-04-22 Diane TroutExtend makebed to lookup metadata out of a copy of... tree | commitdiff
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htsworkflow sequencing LIMS software