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htsworkflow.git
2010-09-30
Diane Trout
Ignore some files generated by python
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2010-09-24
Diane Trout
Adjust spoolwatchers use of inotify to correspond to...
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2010-09-24
Diane Trout
Handle the case when a sequencing lane lacks any yield...
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2010-09-24
Diane Trout
Remind myself that dry-run doesn't work with the extrac...
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2010-09-10
Diane Trout
Add support for CASAVA 1.7
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2010-08-24
Diane Trout
Better detect which program ids generated CNF4 srf...
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2010-08-24
Diane Trout
Split parts of build_fastqs into a seperate function.
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2010-08-23
Diane Trout
Add a "All Lanes" option to the control-lane field...
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2010-08-14
Diane Trout
Shrink flowcell notes field.
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2010-08-14
Diane Trout
Don't offer to track flowcell config files in svn
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2010-08-13
Diane Trout
Remove debug print statement
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2010-08-13
Diane Trout
Reduce the size of the bioanalyzer summary text box
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2010-08-13
Diane Trout
Tell git to ignore *.py[co]~ files.
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2010-08-13
Diane Trout
This patch adds in fields to support storing bioanalyze...
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2010-07-14
Diane Trout
Georgi used slightly different extensions for the secon...
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2010-07-14
Diane Trout
Add search field to the lanes admin page
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2010-07-12
Diane Trout
Use the htsworkflow API to determine if a flowcell...
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2010-07-12
Diane Trout
Under some conditions urlerror doesn't have a code,
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2010-07-12
Diane Trout
Report if a lane was on a paired end flowcell from...
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2010-07-09
Diane Trout
Since srf2named_fastq detects what type of srf file...
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2010-07-08
Diane Trout
Update srf2named_fastq to try to detect if the srf...
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2010-07-08
Diane Trout
Add option to force overwriting old fastqs.
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2010-07-07
Diane Trout
If a quality score started with an @ sign it was treate...
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2010-07-07
Diane Trout
This still isn't ideal as the RESULTS_HOME_DIR is still...
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2010-06-22
Diane Trout
Save changes needed to submit to UCSC in Jun 2010.
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2010-06-22
Diane Trout
Fix srf2named_fastq to output the proper /2 in paired...
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2010-06-15
Diane Trout
Update the 'flowcell started' email message to include...
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2010-06-15
Diane Trout
Make it easier to run srf2named_fastq.py
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2010-06-15
Diane Trout
Wrapper script that helps convert srf files to fastq...
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2010-06-14
Diane Trout
Rename avg_lib_size to gel_cut_size, and add insert_size
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2010-06-14
Diane Trout
Update internal copy of the django admin/templates...
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2010-06-11
Diane Trout
Collect fastqs by read and add them to the configuratio...
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2010-06-11
Diane Trout
Put partial support back in for srf files.
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2010-06-10
Diane Trout
Add script to try and build submissions to the UCSC...
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2010-06-10
Diane Trout
Extend htsworkflow.pipelines.sequences to also try...
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2010-06-10
Diane Trout
Move the code to scan the sequence file archive to...
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2010-06-10
Diane Trout
new api module actually needed logging.
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2010-06-10
Diane Trout
Move the knowledge of the urls for the REST API to...
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2010-06-01
Diane Trout
apparently commas are important
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2010-06-01
Diane Trout
make-library-tree should be an installed script too
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2010-05-29
Diane Trout
Add in extra fields lorian asked for to library detail...
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2010-05-29
Diane Trout
Do not insert anything into the header if there is...
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2010-05-17
Diane Trout
qseq2fastq should also be installed as a script
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2010-05-14
Brandon King
A patch that allows printing more than 11 labels at...
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2010-05-13
Brandon King
Default to pointing to the Ubuntu python location for...
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2010-05-08
Diane Trout
Matches can have trailing AGCT in addition to a number
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2010-05-08
Diane Trout
Always return a count from carefully_make_hardlinks
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2010-05-07
Brandon King
Disabling 'delete selected'.
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2010-04-29
Brandon King
Added a 'Print Labels' action to the Library Admin...
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2010-04-23
Diane Trout
Update summary script to read from the GERALD Summary...
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2010-04-23
Diane Trout
Add support for generating fasta files in addition...
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2010-04-10
Brandon King
WARNING: Django 1.0.2 to Django 1.1.1 compatibility...
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2010-03-22
Diane Trout
Extend qseq2fastq to write to two fastq files,
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2010-03-05
Diane Trout
Report hidden field in the library API
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2010-03-05
Diane Trout
Use the HTS workflow API to figure out the library...
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2010-02-22
Diane Trout
there is no such thing as sequence_extended. I was...
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2010-02-04
Diane Trout
Return affiliation, library name, and comment in the...
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2010-02-04
Diane Trout
Actually implement the code to loop over a list of...
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2010-01-30
Diane Trout
Update the inventory tracker code for the split from...
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2010-01-28
Diane Trout
Adds a json api 'lanes_for' feature
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2010-01-28
Diane Trout
Force auth_backend error messages to sys stderr, as
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2010-01-27
Diane Trout
Remove debugging code that breaks mod_wsgi
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2010-01-26
Diane Trout
Added 'lanes_for' which will show recent flowcell lanes...
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2010-01-22
Diane Trout
Refine user handling.
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2010-01-21
Diane Trout
Update test code to deal with the switch to storing...
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2010-01-21
Diane Trout
Don't throw an error if library.cell_line is None.
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2010-01-13
Diane Trout
Modify qseq2fastq to also read from compressed tar...
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2010-01-07
Diane Trout
Update the usage string for qseq2fastq
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2009-12-15
Diane Trout
Add flowcell/lane information for a library to the...
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2009-12-15
Diane Trout
Define the unicode() function for HTSUser to also repor...
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2009-12-15
Diane Trout
Include information about the flowcell run date on...
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2009-12-15
Diane Trout
Make the basic library page show up when javascript...
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2009-12-15
Diane Trout
Tell people to use the https address so it'll work...
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2009-12-11
Diane Trout
Modify the srf utility to tar.bz2 the qseq files instea...
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2009-12-01
Diane Trout
Replace '.' with 'N' in the sequence from qseq files.
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2009-12-01
Diane Trout
Fix typo in srf command
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2009-12-01
Diane Trout
Also include the read ID in the fastq header
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2009-12-01
Diane Trout
Add a simple utility to convert qseq to fastq files.
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2009-11-25
Diane Trout
Watch for a list of files to indicate that the flowcell...
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2009-11-13
Diane Trout
Override extjs's rather harsh stylesheet so the library...
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2009-11-10
Diane Trout
Don't add the post_run_command unless the option and...
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2009-11-10
Diane Trout
Remport that the pipeline will be done in X to Y days...
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2009-10-27
Diane Trout
update inventory status template to use new field name...
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2009-10-27
Diane Trout
Allow specifying which database to convert
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2009-10-27
Diane Trout
Turn the library_id back into the primary key for sampl...
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2009-10-17
Diane Trout
Figure out the absolute path to the runfolder for passi...
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2009-10-08
Diane Trout
Also use the javascript dual panel choice box for tags.
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2009-10-08
Diane Trout
In some cases test_retrive_config will attempt to norma...
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2009-10-08
Diane Trout
Use raw_id_fields for the library ID in the Flowcell...
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2009-10-08
Diane Trout
Add the ability not to build srf files.
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2009-10-06
Diane Trout
Add an account number field to a library. (Note SCHEMA...
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2009-10-06
Diane Trout
Add a bread crumb to the send started email page.
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2009-10-06
Diane Trout
Remove spurious print
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2009-10-06
Diane Trout
Test that the email notification actually generates...
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2009-10-06
Diane Trout
Use eland_extended or eland_pair instead of eland for...
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2009-10-06
Diane Trout
Default to sequencing if we don't have a genome for...
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2009-10-02
Diane Trout
Test the updated version of extract results that builds...
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2009-09-30
Diane Trout
Add building srf files to runfolder as part of --extrac...
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2009-09-28
Diane Trout
Modify hdquery to not die when being imported on non...
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2009-09-26
Diane Trout
The config file should also set the SEQUENCE_FORMAT
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