Activity for David Trudgian
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David Trudgian committed [40a31b]
Ensure vagrant provision succeeds on non-biohpc machines
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Ignore .vagrant directory
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Separate old 4.6.3 and new 5.1.0 tpp patches
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More vagrant OS deps, and mysql password that fits requirements
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Makefile.PL - update extern downloads. Fixes.
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Updating README
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Remove completed work package directories to li...
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Merge branch 'utsw'
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RemoteSLURM scheduler - now working with TACC S...
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WIP: RemoteSLURM Shepherd to use TACC Stampede ...
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Merge branch 'utsw'
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Fix INSTALL text about creating main cpfp.conf ...
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Add brief admin tutorial documents which were o...
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Ugly fix for Carp::Heavy site/local version mis...
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Merge branch 'utsw' of proteomics-srv-01.swmed....
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Update default instrument definitions
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See commit [af8876]
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More up-to-date / useful instrument definitions...
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Install instructions for Ubuntu
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Queries from others interested have died down. New build process that downloads CPFP,...
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Isolated to UTSW install CPAN module versions. Working fine on fresh installs and...
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Fix / Replace AutoCRUD admin screen for instruments etc
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Added MySQL workbench file and EER PDF [43a2f66]
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Create ER Diagram
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Add MySQL workbench model and ER diagram PDF fo...
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Remove UTSW and Oxford logos to comply with res...
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Rudimentary help message added.
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CLI should show supported actions for SCH/MSS/TSK etc.
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Add rudimentary help message for cpfp_cli.pl
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UTSW branch Makefile.PL now throws errors / downloads MyriMatch.
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Makefile must check for unzip
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UTSW branch Makefile now throws errors / downloads MyriMatch.
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Provide TokuDB conversion script in distro
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UTSW install is only one using TokuDB. Compression is nice, but no real performance...
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Alternative protein inference algorithm
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Scale back ambitions with DCT leaving UTSW. Not required for ongoing work.
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Believe (2) is fixed now - not experienced at UTSW for at least past 3 months. Unsure...
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Export mzIdentML
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Good enough for UTSW purposes as of [d825cf]
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Implement export to MzIdentML instead.
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SQLite Export of Submission
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Allow DBIC search attrs to be passed in to psm_...
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WIP: Prototype script for export of MSS results...
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Add option to initialize a Bio::DB::Fasta index...
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Make mzid contact info/org/person stuff generic...
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Ooops. Create scripts shouldn't include UniMod ...
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Add missing XML::Writer CPAN dep needed for MzI...
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Adding create SQL script for schema 2.1.1
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WIP: Integrate AS mzid export work as a Task Pr...
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WIP working mzidentml for perSPECtives
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Increment version number to 2.1.1 for final tes...
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Merge branch 'utsw' of proteomics-srv-01.swmed....
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Merge branch 'utsw' of prcvlx-login-01.swmed.ed...
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Remove InnoDB Baraccuda/Compressed docs in INST...
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Merge branch 'utsw' of ssh://git.code.sf.net/p/...
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Syntax error in cpanfile
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Merge branch 'utsw' of prcvlx-login-01.swmed.ed...
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Force /bin/sh shell in execution of daemons in ...
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Install FCGI.pm from CPAN so that fastcgi insta...
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Correct installation docs according to AS test ...
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Correct import_unimod.pl after previous removal...
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Doh! import_unimod.pl needs a connected schema ...
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Merge branch 'oxford' of ssh://git.code.sf.net/...
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Merge remote branch 'sf/oxford' into utsw
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Force protein accession and description columns...
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Merge branch 'utsw' of /srv/git/cpfp into utsw
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Fix results loading screens so any errors are displayed on Excel export
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Fix 'related resultsource is not registered wit...
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Potential div0 error in PepXMLImport
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Looks good to me. Was merged into UTSW branch.
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Hacked together some code to get mzIdentML from searches (not MSS yet) that will...
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ModLS replacement / major improvement
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[63c7ba] Fixed some errors introduced to ModLS, e.g. incorrect use of losses. Now...
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Dennis Mungai Suggested Changes
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Fixed [e491b1]
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Fix install issues noted by Dennis Mungai [#43]
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Fix MSGF+ download URL (moved)
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Allow access to PeptideProphet Accurate Mass Mo...
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Bug - correct flags for PeptideProphet are not being passed
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Fixed [b03619f]
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Fixed b03619f
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Merge branch 'oxford' of ssh://git.code.sf.net/...
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Fix bug #48 - make sure correct flags are passe...
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Bug - correct flags for PeptideProphet are not being passed
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Bug - correct flags for PeptideProphet are not being passed
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Troubleshooting intermittent state crossoever -...
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Apply target/decoy ratio fix for meta-searches,...
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Troubleshooting intermittent state crossover - ...
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Troubleshooting intermittent state crossover - ...
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Troubleshooting intermittent state crossover - ...
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Remove experimental and modification notes for ...
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Write neutral loss information for modification...
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Add HTTP_PROXY config var for Mascot http requests
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Update Makefile.PL - Download MyriMatch, Downlo...
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COMET: Write out a much more full comet.params ...
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MyriMatch Searches : Disable 13C MonoisotopeAdj...
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TPP - ProphetModels decoy ratio parameter is to...
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Fix fragment calculation and plotting so MH pea...
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Pass name of local downloaded unimod.xml file a...
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Mascot - Allow submission to a server using Mas...
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