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2010-10-19	Diane Trout	Set WITH_SEQUENCE as both a per-lane AND global parameter	commit \| commitdiff \| tree
2010-10-08	Diane Trout	WITH_SEQUENCE is actually a global GERALD option, remove...	commit \| commitdiff \| tree
2010-10-07	Diane Trout	Update gerald config file generation.	commit \| commitdiff \| tree
2010-09-30	Diane Trout	Ignore some files generated by python	commit \| commitdiff \| tree
2010-09-24	Diane Trout	Adjust spoolwatchers use of inotify to correspond to...	commit \| commitdiff \| tree
2010-09-24	Diane Trout	Handle the case when a sequencing lane lacks any yield...	commit \| commitdiff \| tree
2010-09-24	Diane Trout	Remind myself that dry-run doesn't work with the extract...	commit \| commitdiff \| tree
2010-09-10	Diane Trout	Add support for CASAVA 1.7	commit \| commitdiff \| tree
2010-08-24	Diane Trout	Better detect which program ids generated CNF4 srf...	commit \| commitdiff \| tree
2010-08-24	Diane Trout	Split parts of build_fastqs into a seperate function.	commit \| commitdiff \| tree
2010-08-23	Diane Trout	Add a "All Lanes" option to the control-lane field...	commit \| commitdiff \| tree
2010-08-14	Diane Trout	Shrink flowcell notes field.	commit \| commitdiff \| tree
2010-08-14	Diane Trout	Don't offer to track flowcell config files in svn	commit \| commitdiff \| tree
2010-08-13	Diane Trout	Remove debug print statement	commit \| commitdiff \| tree
2010-08-13	Diane Trout	Reduce the size of the bioanalyzer summary text box	commit \| commitdiff \| tree
2010-08-13	Diane Trout	Tell git to ignore *.py[co]~ files.	commit \| commitdiff \| tree
2010-08-13	Diane Trout	This patch adds in fields to support storing bioanalyzer...	commit \| commitdiff \| tree
2010-07-14	Diane Trout	Georgi used slightly different extensions for the second...	commit \| commitdiff \| tree
2010-07-14	Diane Trout	Add search field to the lanes admin page	commit \| commitdiff \| tree
2010-07-12	Diane Trout	Use the htsworkflow API to determine if a flowcell...	commit \| commitdiff \| tree
2010-07-12	Diane Trout	Under some conditions urlerror doesn't have a code,	commit \| commitdiff \| tree
2010-07-12	Diane Trout	Report if a lane was on a paired end flowcell from...	commit \| commitdiff \| tree
2010-07-09	Diane Trout	Since srf2named_fastq detects what type of srf file...	commit \| commitdiff \| tree
2010-07-08	Diane Trout	Update srf2named_fastq to try to detect if the srf...	commit \| commitdiff \| tree
2010-07-08	Diane Trout	Add option to force overwriting old fastqs.	commit \| commitdiff \| tree
2010-07-07	Diane Trout	If a quality score started with an @ sign it was treated...	commit \| commitdiff \| tree
2010-07-07	Diane Trout	This still isn't ideal as the RESULTS_HOME_DIR is still...	commit \| commitdiff \| tree
2010-06-22	Diane Trout	Save changes needed to submit to UCSC in Jun 2010.	commit \| commitdiff \| tree
2010-06-22	Diane Trout	Fix srf2named_fastq to output the proper /2 in paired...	commit \| commitdiff \| tree
2010-06-15	Diane Trout	Update the 'flowcell started' email message to include...	commit \| commitdiff \| tree
2010-06-15	Diane Trout	Make it easier to run srf2named_fastq.py	commit \| commitdiff \| tree
2010-06-15	Diane Trout	Wrapper script that helps convert srf files to fastq...	commit \| commitdiff \| tree
2010-06-14	Diane Trout	Rename avg_lib_size to gel_cut_size, and add insert_size	commit \| commitdiff \| tree
2010-06-14	Diane Trout	Update internal copy of the django admin/templates...	commit \| commitdiff \| tree
2010-06-11	Diane Trout	Collect fastqs by read and add them to the configuration...	commit \| commitdiff \| tree
2010-06-11	Diane Trout	Put partial support back in for srf files.	commit \| commitdiff \| tree
2010-06-10	Diane Trout	Add script to try and build submissions to the UCSC...	commit \| commitdiff \| tree
2010-06-10	Diane Trout	Extend htsworkflow.pipelines.sequences to also try...	commit \| commitdiff \| tree
2010-06-10	Diane Trout	Move the code to scan the sequence file archive to...	commit \| commitdiff \| tree
2010-06-10	Diane Trout	new api module actually needed logging.	commit \| commitdiff \| tree
2010-06-10	Diane Trout	Move the knowledge of the urls for the REST API to...	commit \| commitdiff \| tree
2010-06-01	Diane Trout	apparently commas are important	commit \| commitdiff \| tree
2010-06-01	Diane Trout	make-library-tree should be an installed script too	commit \| commitdiff \| tree
2010-05-29	Diane Trout	Add in extra fields lorian asked for to library detail...	commit \| commitdiff \| tree
2010-05-29	Diane Trout	Do not insert anything into the header if there is...	commit \| commitdiff \| tree
2010-05-17	Diane Trout	qseq2fastq should also be installed as a script	commit \| commitdiff \| tree
2010-05-08	Diane Trout	Matches can have trailing AGCT in addition to a number	commit \| commitdiff \| tree
2010-05-08	Diane Trout	Always return a count from carefully_make_hardlinks	commit \| commitdiff \| tree
2010-04-23	Diane Trout	Update summary script to read from the GERALD Summary...	commit \| commitdiff \| tree
2010-04-23	Diane Trout	Add support for generating fasta files in addition...	commit \| commitdiff \| tree
2010-03-22	Diane Trout	Extend qseq2fastq to write to two fastq files,	commit \| commitdiff \| tree
2010-03-05	Diane Trout	Report hidden field in the library API	commit \| commitdiff \| tree
2010-03-05	Diane Trout	Use the HTS workflow API to figure out the library...	commit \| commitdiff \| tree
2010-02-22	Diane Trout	there is no such thing as sequence_extended. I was...	commit \| commitdiff \| tree
2010-02-04	Diane Trout	Return affiliation, library name, and comment in the...	commit \| commitdiff \| tree
2010-02-04	Diane Trout	Actually implement the code to loop over a list of...	commit \| commitdiff \| tree
2010-01-30	Diane Trout	Update the inventory tracker code for the split from...	commit \| commitdiff \| tree
2010-01-28	Diane Trout	Adds a json api 'lanes_for' feature	commit \| commitdiff \| tree
2010-01-28	Diane Trout	Force auth_backend error messages to sys stderr, as	commit \| commitdiff \| tree
2010-01-27	Diane Trout	Remove debugging code that breaks mod_wsgi	commit \| commitdiff \| tree
2010-01-26	Diane Trout	Added 'lanes_for' which will show recent flowcell lanes...	commit \| commitdiff \| tree
2010-01-22	Diane Trout	Refine user handling.	commit \| commitdiff \| tree
2010-01-21	Diane Trout	Update test code to deal with the switch to storing...	commit \| commitdiff \| tree
2010-01-21	Diane Trout	Don't throw an error if library.cell_line is None.	commit \| commitdiff \| tree
2010-01-13	Diane Trout	Modify qseq2fastq to also read from compressed tar...	commit \| commitdiff \| tree
2010-01-07	Diane Trout	Update the usage string for qseq2fastq	commit \| commitdiff \| tree
2009-12-15	Diane Trout	Add flowcell/lane information for a library to the...	commit \| commitdiff \| tree
2009-12-15	Diane Trout	Define the unicode() function for HTSUser to also report...	commit \| commitdiff \| tree
2009-12-15	Diane Trout	Include information about the flowcell run date on...	commit \| commitdiff \| tree
2009-12-15	Diane Trout	Make the basic library page show up when javascript...	commit \| commitdiff \| tree
2009-12-15	Diane Trout	Tell people to use the https address so it'll work...	commit \| commitdiff \| tree
2009-12-11	Diane Trout	Modify the srf utility to tar.bz2 the qseq files instead...	commit \| commitdiff \| tree
2009-12-01	Diane Trout	Replace '.' with 'N' in the sequence from qseq files.	commit \| commitdiff \| tree
2009-12-01	Diane Trout	Fix typo in srf command	commit \| commitdiff \| tree
2009-12-01	Diane Trout	Also include the read ID in the fastq header	commit \| commitdiff \| tree
2009-12-01	Diane Trout	Add a simple utility to convert qseq to fastq files.	commit \| commitdiff \| tree
2009-11-25	Diane Trout	Watch for a list of files to indicate that the flowcell...	commit \| commitdiff \| tree
2009-11-13	Diane Trout	Override extjs's rather harsh stylesheet so the library...	commit \| commitdiff \| tree
2009-11-10	Diane Trout	Don't add the post_run_command unless the option and...	commit \| commitdiff \| tree
2009-11-10	Diane Trout	Remport that the pipeline will be done in X to Y days...	commit \| commitdiff \| tree
2009-10-27	Diane Trout	update inventory status template to use new field name...	commit \| commitdiff \| tree
2009-10-27	Diane Trout	Allow specifying which database to convert	commit \| commitdiff \| tree
2009-10-27	Diane Trout	Turn the library_id back into the primary key for samples_li...	commit \| commitdiff \| tree
2009-10-17	Diane Trout	Figure out the absolute path to the runfolder for passing...	commit \| commitdiff \| tree
2009-10-08	Diane Trout	Also use the javascript dual panel choice box for tags.	commit \| commitdiff \| tree
2009-10-08	Diane Trout	In some cases test_retrive_config will attempt to normalize...	commit \| commitdiff \| tree
2009-10-08	Diane Trout	Use raw_id_fields for the library ID in the Flowcell...	commit \| commitdiff \| tree
2009-10-08	Diane Trout	Add the ability not to build srf files.	commit \| commitdiff \| tree
2009-10-06	Diane Trout	Add an account number field to a library. (Note SCHEMA...	commit \| commitdiff \| tree
2009-10-06	Diane Trout	Add a bread crumb to the send started email page.	commit \| commitdiff \| tree
2009-10-06	Diane Trout	Remove spurious print	commit \| commitdiff \| tree
2009-10-06	Diane Trout	Test that the email notification actually generates...	commit \| commitdiff \| tree
2009-10-06	Diane Trout	Use eland_extended or eland_pair instead of eland for...	commit \| commitdiff \| tree
2009-10-06	Diane Trout	Default to sequencing if we don't have a genome for...	commit \| commitdiff \| tree
2009-10-02	Diane Trout	Test the updated version of extract results that builds...	commit \| commitdiff \| tree
2009-09-30	Diane Trout	Add building srf files to runfolder as part of --extract...	commit \| commitdiff \| tree
2009-09-28	Diane Trout	Modify hdquery to not die when being imported on non...	commit \| commitdiff \| tree
2009-09-26	Diane Trout	The config file should also set the SEQUENCE_FORMAT	commit \| commitdiff \| tree
2009-09-26	Diane Trout	HttpRequest.getcode doesn't exist in python 2.4, use...	commit \| commitdiff \| tree
2009-09-26	Diane Trout	Implement a client side config file generator.	commit \| commitdiff \| tree
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