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Wrapper script that helps convert srf files to fastq files.
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 configuration...
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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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2010-05-08
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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2010-04-23
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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2010-03-22
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 report...
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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 instead...
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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 samples_li...
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2009-10-17
Diane Trout
Figure out the absolute path to the runfolder for passing...
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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 normalize...
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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 --extract...
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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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2009-09-26
Diane Trout
HttpRequest.getcode doesn't exist in python 2.4, use...
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2009-09-26
Diane Trout
Implement a client side config file generator.
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2009-09-26
Diane Trout
Print library.library_id instead of the flowcell.library_id.
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2009-09-23
Diane Trout
Return species information as part of the flowcell...
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2009-09-19
Diane Trout
Put a stub species_json in, as I'd listed it in the...
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2009-09-19
Diane Trout
Allow grabbing library information via json.
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2009-09-19
Diane Trout
Add a /config/<fcid>/json url that returns information...
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2009-09-19
Diane Trout
Django really wanted a 404 template.
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2009-09-16
Diane Trout
Force addition of HTSUser object if someone is creating...
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2009-09-16
Diane Trout
Replace some prints with logging.info messages and
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2009-09-14
Diane Trout
Fix ticket:145 this patch includes the tar.bz2 extension...
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2009-09-11
Diane Trout
Apparently I should've rendered the emails in plain...
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2009-09-11
Diane Trout
None is better than a baddly munged string for when...
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2009-09-10
Diane Trout
Don't crash if there are no lane result summary entries...
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2009-09-10
Diane Trout
Report if the Summary.htm file is missing the Lane...
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2009-09-10
Diane Trout
Remove spurious pring debugging statements as they...
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2009-09-02
Diane Trout
remove spurious debug print statement
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2009-09-01
Diane Trout
Report who the site managers are for the BCC
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2009-08-22
Diane Trout
Now adding a user adds the key linking the htsuser...
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2009-08-20
Diane Trout
Implement a send started email feature.
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2009-08-20
Diane Trout
Reorder imports in model to make me happy.
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2009-08-19
Diane Trout
Use hasattr instead of checking for django version...
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2009-08-19
Diane Trout
Forgot to update one request to request.REQUEST variable...
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2009-08-19
Diane Trout
Convert stanford/hudson alpha's updStatus to work with...
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2009-08-18
Diane Trout
Update hudson alpha's eland config file generator to...
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2009-08-18
Diane Trout
Update eland_config generator to work with the new...
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2009-08-18
Diane Trout
Update Rami's flowcell report to work with our new...
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2009-08-18
Diane Trout
Add a custom (inherited) user object named HTSUser...
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2009-08-18
Diane Trout
Fix code where the python str() function had been overridden...
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2009-08-12
Diane Trout
Converted Brandon's scripts into a single python script...
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2009-08-12
Diane Trout
Move Brandon's upgrade script in with all the other...
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2009-07-23
Diane Trout
ReadPreps can also use the netcopy complete flags which...
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2009-07-21
Diane Trout
Allow specifying the we're finished sequencing file...
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