Activity for Paolo Amedeo
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Paolo Amedeo committed [bcc09b]
Modified queries pulling database names and usage from
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Introduced changes in Perl scripts to accommodate for archived
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Fixed a typo in query in TIGR::GLKLib.pm and cleaned up code in two Perl
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GLKLib.pm - changed query for getting all VGD databases to check in
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A few more changes to archiveSamples.pl to make it working independently
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Added option for archiving also samples having a sample ID not found in
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runDeepSequencingAnalysis.pl - Modified code not to hang in the case
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findVariants.pl - Corrected bug in frequency on call to CLC
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runDeepSequencingAnalysis.pl - fixed bug causing infinite loop on
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findVariants.pl - modified to allow handling "extended BAC ID" (i.e.
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Added wait time between grid job submissions, in order to minimize
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Corrected CLC scratch path in DSA scripts
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Added --include_pending_sra option to
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Merge branch 'master' of ssh://pamedeo@git.code.sf.net/p/elvira/git
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Added script Extract_Low_Coverage_Areas.pl which parses autoTasker2
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Merge branch 'master' of ssh://pamedeo@git.code.sf.net/p/elvira/git
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Create_Tuples_For_SRA_Submission.pl - Corrected bug (tuples of samples
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Create_Tuples_For_SRA_Submission.pl - Implemented splitting
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Added Create_Tuples_For_SRA_Submission.pl - Script that creates tuple
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TIGR::GLKLib.pm - fixed bug in call to isValidBioProject()
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TIGR::GLKLib.pm Updated list of attributes where Missing and Unknown are
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TIGR::GLKLib.pm - Changed signature of isValidBioProject() as part of
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Merge branch 'master' of ssh://pamedeo@git.code.sf.net/p/elvira/git
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TIGR::GLKLib.pm Updated lists of attributes accepting "Unknown" and
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Merge branch 'master' of ssh://pamedeo@git.code.sf.net/p/elvira/git
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Load_SRA_IDs.pl - Updated the headers and the documentation, and
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Load_SRA_IDs.pl - Updated the headers and the documentation, and
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TIGR::GLKLib.pm - "reactivated" isUmbrellaBioProject() function
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Find_Samples_Without_Normalized_Host.pl & Update_ExtentAttribute.pl -
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Prepare_SRA_Submission_Template.pl - Fixed bug in simulation (output
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Merge branch 'SRA_Pipeline'
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Merge branch 'master' of ssh://pamedeo@git.code.sf.net/p/elvira/git
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Load_SRA_IDs.pl - intermediary commit not to loose changes.
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Merge remote-tracking branch 'origin/master' into SRA_Pipeline
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archiveSamples.pl - Improved handling of "look-alike" directories and
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Updated classpath
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Switching from jdbc4 to jdbc3
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This is just a test branch testing earlier implementation of Sybase jdbc
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Removed duplicates from Normalized_Host.map
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Removed $BUILD variable, being uninitialized due to Git not handling
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Updated the lookup list for normalized hosts and improved the script
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Adding missing external libraries. Updating version string for
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Corrected typo in new value for ExtentAttributeType.value_type
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Load_SRA_IDs.pl - More code development, but still not complete.
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Load_SRA_IDs.pl - working version.
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First (incomplete) draft of Load_SRA_IDs.pl
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Added components for the Long Oligo pipeline.
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Fixed bug in hybrid2-x.pl
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Added Prepare_SRA_Submission_Template.pl - This script is in a
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More cleanup.
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Merge remote-tracking branch 'origin/master'
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Testing merging locally
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Fixed bugs in archiveSamples.pl (VHTNGS-1427)
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Lemur - Several improvements, ranging from visual (hiding from drop-down selection unused Extent_Type values) to functional (movint to vir_common.php all the functions dealing with tables in vir_common, adding functions to update Collection table), fixing bug of not updating collection ID in vir_common (ELVIRA-147)
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