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Modify qseq2fastq to also read from compressed tar files containing qseq files
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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2009-07-01
Diane Trout
Add LibraryType option, (this will probably require...
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2009-07-01
Diane Trout
Change the cluster station default to the current working...
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2009-06-30
Diane Trout
Allow cellline and conditition to be blank [ticket...
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2009-06-30
Diane Trout
Provide a dummy eland result lane class if there's...
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2009-06-23
Diane Trout
The url validation code wasn't working on python2.4
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2009-06-20
Diane Trout
Send the specific directory that needs to be copied...
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2009-06-19
Diane Trout
I started using ResultLane, so stop treating it like...
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2009-06-17
Diane Trout
Add support for extracting data out of Illumina's new...
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2009-06-17
Diane Trout
Add a hack to add a frontend section if not present
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2009-06-17
Diane Trout
Loading really old run xml files caused the website...
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2009-06-17
Diane Trout
Ignore *.py[co~] files to make svn status happier
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2009-06-17
Diane Trout
Add stub uuid function to make this module import when...
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2009-06-17
Diane Trout
remove spurious debug print statements
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2009-06-16
Diane Trout
The error being thrown by benderjab changed slightly.
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2009-06-16
Diane Trout
Split rsync initialization out of run so we can test
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2009-06-16
Diane Trout
Fixed a couple of problems.
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2009-06-16
Diane Trout
Update test copier code for the changes in the copier...
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2009-06-15
Diane Trout
Allow searching by library name on the experiments...
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2009-06-10
Diane Trout
Scan more than one rsync repository for directory trees...
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2009-06-09
Diane Trout
Add code to construct a copy url using a mapping in...
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2009-06-05
Diane Trout
Pyinotify behaves oddly when the stdio file descriptors...
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2009-06-01
Diane Trout
Consistently use 'watchdir' instead of 'watch_dir'...
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2009-05-30
Diane Trout
Watch more than one directory tree for modification.
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2009-05-30
Diane Trout
Don't print the discovered mount point.
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2009-05-27
Diane Trout
Add a minimal test case to test a small bit of the...
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2009-05-11
Diane Trout
More consistently split the flowcell id and status...
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2009-05-11
Diane Trout
Fix parameter list for base class.
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2009-05-06
Diane Trout
Update htsworkflow.util.fctracker module to work with...
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2009-05-05
Diane Trout
Update the django app to report "raw reads" for a sequence...
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2009-05-05
Diane Trout
Handle lanes that were only sequenced.
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2009-05-05
Diane Trout
Return NaN, NaN if a mean +/- deviation value was undefined...
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2009-05-05
Diane Trout
Allow overriding the queued commands environment.
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2009-05-01
Diane Trout
Add wait_for_ipar option to the spool watcher config...
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