Activity for Central Proteomics Facilities Pipeline

David Trudgian committed [a78b06]

David Trudgian — Thu, 03 Jan 2019 20:03:38 -0000

Working LocalSLURM Sheperd

David Trudgian committed [44d7c3]

David Trudgian — Thu, 03 Jan 2019 20:03:38 -0000

Vagrant - use 2.2.0 db create script

David Trudgian committed [650f8f]

David Trudgian — Thu, 03 Jan 2019 20:03:38 -0000

Fix RemoteSGE log message typo

David Trudgian committed [12eb85]

David Trudgian — Thu, 03 Jan 2019 20:03:38 -0000

Patch Tandem2XML to pull scan nums from name.start.end.charge format descr

David Trudgian committed [f45136]

David Trudgian — Thu, 03 Jan 2019 20:03:38 -0000

Tidy Makefile.PL

David Trudgian committed [0325a1]

David Trudgian — Thu, 03 Jan 2019 20:03:38 -0000

LocalSLURM sheperd

David Trudgian committed [e9fabf]

David Trudgian — Thu, 03 Jan 2019 20:03:38 -0000

Strip RTINSECONDS=99.99 from Tandem output

David Trudgian committed [5944bd]

David Trudgian — Thu, 03 Jan 2019 20:03:38 -0000

Add Local/RemoteSLURM notes to INSTALL(.pod)

David Trudgian committed [66aaa7]

David Trudgian — Mon, 31 Dec 2018 20:10:23 -0000

Vagrant - set 'sql-mode=' in my.cnf

David Trudgian committed [96fef9]

David Trudgian — Mon, 31 Dec 2018 20:06:36 -0000

Vagrant - install NCBI Blast+

David Trudgian committed [43bd03]

David Trudgian — Mon, 31 Dec 2018 19:51:10 -0000

Make TTP-5.1.0 patches apply on generic system

David Trudgian committed [795dc2]

David Trudgian — Mon, 31 Dec 2018 19:50:36 -0000

Missing : on FindBin::lib

David Trudgian committed [91c7bd]

David Trudgian — Mon, 31 Dec 2018 19:38:40 -0000

Missing : on FindBin::lib

astrocyte committed [3dacf3]

astrocyte — Mon, 31 Dec 2018 19:23:09 -0000

Merge branch 'utsw-biohpc' of https://github.com/dctrud/cpfp into utsw-biohpc

David Trudgian committed [f5a76d]

David Trudgian — Mon, 31 Dec 2018 19:23:09 -0000

Merge remote-tracking branch 'dct/utsw-biohpc' into utsw-biohpc

David Trudgian committed [c9c02d]

David Trudgian — Mon, 31 Dec 2018 19:21:35 -0000

Vagrant - drop hyper-v config, too many issues

David Trudgian committed [9a2e82]

David Trudgian — Mon, 31 Dec 2018 19:00:48 -0000

Merge branch 'utsw-biohpc' of ssh://git.code.sf.net/p/cpfp/code into utsw-biohpc

David Trudgian committed [a52ea0]

David Trudgian — Fri, 28 Dec 2018 21:22:57 -0000

Bump version to 2.2.0 as we have changed much

David Trudgian committed [c41189]

David Trudgian — Fri, 28 Dec 2018 21:20:13 -0000

Bump version to 2.2.0 as we have changed much

David Trudgian committed [1f7379]

David Trudgian — Fri, 28 Dec 2018 21:07:14 -0000

MSGFPlus -m for HCD<->ETD has swapped 2<->3

David Trudgian committed [b87d2d]

David Trudgian — Fri, 28 Dec 2018 21:00:24 -0000

Install FindBin::lib from cpan for TPP 5.1.0

David Trudgian committed [f1abfc]

David Trudgian — Fri, 28 Dec 2018 20:59:01 -0000

Changes to TPP calls for TPP 5.1.0

David Trudgian committed [e3e8ec]

David Trudgian — Fri, 28 Dec 2018 19:30:08 -0000

Missing sdb_is_active in create_2.1.2.sql

David Trudgian committed [cbf2b5]

David Trudgian — Fri, 28 Dec 2018 19:26:05 -0000

Vagrant - need libpng12-devel

David Trudgian committed [eacdf3]

David Trudgian — Fri, 28 Dec 2018 19:19:18 -0000

Patch TPP 5.1.0 CProteinAmbiguityGroup.cpp to compile on EL 7

David Trudgian committed [3c9286]

David Trudgian — Thu, 27 Dec 2018 20:52:35 -0000

More logging in Makefile.PL

David Trudgian committed [6afe5d]

David Trudgian — Thu, 27 Dec 2018 20:25:31 -0000

Vagrant - enable hyperv provider

David Trudgian committed [a067dd]

David Trudgian — Thu, 27 Dec 2018 20:25:31 -0000

Vagrant - config file and default password file

David Trudgian committed [0c8564]

David Trudgian — Thu, 27 Dec 2018 20:25:31 -0000

Vagrant provision DB and conf file

David Trudgian committed [d428ad]

David Trudgian — Thu, 27 Dec 2018 20:25:31 -0000

Vagrant - smb file share for hyperv

David Trudgian committed [76ea53]

David Trudgian — Thu, 27 Dec 2018 20:25:31 -0000

Net::LDAP is a dependency

David Trudgian committed [d2ff9a]

David Trudgian — Thu, 27 Dec 2018 20:25:31 -0000

Vagrant use centos/7 official with 2GB RAM

David Trudgian committed [55aaf7]

David Trudgian — Thu, 27 Dec 2018 20:25:31 -0000

Vagrant dev server port is 3000 not 8000

David Trudgian committed [0221c2]

David Trudgian — Thu, 27 Dec 2018 18:12:41 -0000

Vagrant dev server port is 3000 not 8000

David Trudgian committed [8880aa]

David Trudgian — Wed, 26 Dec 2018 21:49:56 -0000

Vagrant - smb file share for hyperv

David Trudgian committed [d369d7]

David Trudgian — Wed, 26 Dec 2018 21:49:56 -0000

Vagrant - config file and default password file

David Trudgian committed [e661ea]

David Trudgian — Wed, 26 Dec 2018 21:49:56 -0000

Net::LDAP is a dependency

David Trudgian committed [526c62]

David Trudgian — Wed, 26 Dec 2018 19:53:53 -0000

Vagrant - enable hyperv provider

David Trudgian committed [bd2f45]

David Trudgian — Wed, 26 Dec 2018 19:36:29 -0000

Vagrant provision DB and conf file

David Trudgian committed [8f98c5]

David Trudgian — Wed, 26 Dec 2018 19:36:29 -0000

Vagrant use centos/7 official with 2GB RAM

David Trudgian committed [40a31b]

David Trudgian — Sun, 23 Dec 2018 00:50:49 -0000

Ensure vagrant provision succeeds on non-biohpc machines

David Trudgian committed [23c3ed]

David Trudgian — Sun, 23 Dec 2018 00:50:49 -0000

Ignore .vagrant directory

David Trudgian committed [16a455]

David Trudgian — Sun, 23 Dec 2018 00:50:49 -0000

More vagrant OS deps, and mysql password that fits requirements

David Trudgian committed [217dfe]

David Trudgian — Sun, 23 Dec 2018 00:50:49 -0000

Separate old 4.6.3 and new 5.1.0 tpp patches

David Trudgian committed [2f9b83]

David Trudgian — Sun, 23 Dec 2018 00:50:49 -0000

Makefile.PL - update extern downloads. Fixes.

Central Proteomics Facilities Pipeline released /resources/tpp/TPP_5.1.0-src.tar.gz

Central Proteomics Facilities Pipeline — Sat, 22 Dec 2018 15:00:04 -0000

Central Proteomics Facilities Pipeline released /resources/TPP_5.1.0-src.tar.gz

Central Proteomics Facilities Pipeline — Sat, 22 Dec 2018 14:47:05 -0000

Central Proteomics Facilities Pipeline released /resources/omssa/disclaimer.txt

Central Proteomics Facilities Pipeline — Sat, 22 Dec 2018 14:41:02 -0000

Central Proteomics Facilities Pipeline released /resources/omssa/omssa-linux.tar.gz

Central Proteomics Facilities Pipeline — Sat, 22 Dec 2018 14:41:02 -0000

Central Proteomics Facilities Pipeline released /resources/myrimatch/PWIZ_LICENSE.rtf

Central Proteomics Facilities Pipeline — Sat, 22 Dec 2018 14:39:02 -0000

Central Proteomics Facilities Pipeline released /resources/pwiz/PWIZ_LICENSE.rtf

Central Proteomics Facilities Pipeline — Sat, 22 Dec 2018 14:39:02 -0000

Central Proteomics Facilities Pipeline released /resources/pwiz/pwiz-bin-linux-x86_64-gcc48-release-3_0_18355_621fb05.tar.bz2

Central Proteomics Facilities Pipeline — Sat, 22 Dec 2018 14:37:02 -0000

Central Proteomics Facilities Pipeline released /resources/msgfplus/LICENSE.txt

Central Proteomics Facilities Pipeline — Sat, 22 Dec 2018 14:35:02 -0000

Central Proteomics Facilities Pipeline released /resources/msgfplus/MSGFPlus_v20181015.zip

Central Proteomics Facilities Pipeline — Sat, 22 Dec 2018 14:35:02 -0000

Central Proteomics Facilities Pipeline released /resources/myrimatch/bumbershoot-bin-linux-gcc48-release-3_0.tar.bz2

Central Proteomics Facilities Pipeline — Sat, 22 Dec 2018 14:35:02 -0000

Central Proteomics Facilities Pipeline released /resources/MSGFPlus_v20181015.zip

Central Proteomics Facilities Pipeline — Sat, 22 Dec 2018 14:33:02 -0000

Central Proteomics Facilities Pipeline released /resources/omssa.tar.gz

Central Proteomics Facilities Pipeline — Sat, 22 Dec 2018 14:31:01 -0000

Central Proteomics Facilities Pipeline released /resources/pwiz-bin-linux-x86_64-gcc48-release-3_0_18355_621fb05.tar.bz2

Central Proteomics Facilities Pipeline — Sat, 22 Dec 2018 14:31:01 -0000

Central Proteomics Facilities Pipeline released /resources/bumbershoot-bin-linux-gcc48-release-3_0.tar.bz2

Central Proteomics Facilities Pipeline — Sat, 22 Dec 2018 14:30:02 -0000

David Trudgian committed [1a2654]

David Trudgian — Fri, 21 Dec 2018 22:52:32 -0000

Add basic vagrant setup

David Trudgian committed [3c2d0f]

David Trudgian — Fri, 21 Dec 2018 22:52:32 -0000

.gitignore for Jetbrains .idea dir

David Trudgian committed [02c7d5]

David Trudgian — Fri, 21 Dec 2018 22:44:54 -0000

Output errors from install steps properly

David Trudgian committed [1722b0]

David Trudgian — Fri, 21 Dec 2018 22:44:54 -0000

Disable Myrimatch for now... old URI is bad

David Trudgian committed [24a822]

David Trudgian — Fri, 21 Dec 2018 22:44:54 -0000

Whoops - fix command exit code check

Phil Charles committed [c56d08]

Phil Charles — Mon, 20 Mar 2017 12:23:20 -0000

Modify POSTing of data by Mascot plugin to the ...

Phil Charles committed [223277]

Phil Charles — Thu, 21 Apr 2016 11:11:43 -0000

Allow administrator users to grant submission a...

Phil Charles committed [74a921]

Phil Charles — Thu, 21 Apr 2016 11:11:43 -0000

Fix ModLS bug when including terminal modificat...

Phil Charles committed [195a3e]

Phil Charles — Tue, 03 Nov 2015 15:53:52 -0000

Refactor javascript file uploader to clean up c...

Phil Charles committed [50c486]

Phil Charles — Tue, 22 Sep 2015 14:51:48 -0000

Fixes to LDAP username lookup to handle large n...

Phil Charles committed [f52e86]

Phil Charles — Tue, 22 Sep 2015 14:51:48 -0000

Merge branch 'oxford'

Phil Charles committed [818cc3]

Phil Charles — Tue, 22 Sep 2015 14:51:48 -0000

Fix running SINQ Task via CLI if {CPFP_THREADS}...

Phil Charles committed [4ae662]

Phil Charles — Tue, 22 Sep 2015 14:51:48 -0000

Schema update to v2.1.2; Add support for flaggi...

Phil Charles committed [ef419f]

Phil Charles — Tue, 22 Sep 2015 14:51:48 -0000

Remove unused variable and fix comments printi...

Phil Charles committed [076d36]

Phil Charles — Tue, 22 Sep 2015 14:51:48 -0000

Add some handling for edge-case scenarios where...

Phil Charles committed [1d8c9d]

Phil Charles — Wed, 03 Dec 2014 00:28:55 -0000

Merge branch 'oxford'

Phil Charles committed [f4679f]

Phil Charles — Mon, 01 Dec 2014 17:46:17 -0000

Bugfix add_public_database script to correctly ...

Phil Charles modified ticket #33

Phil Charles — Thu, 23 Oct 2014 12:37:05 -0000

Disordered list in db search submission

Phil Charles posted a comment on ticket #14

Phil Charles — Thu, 23 Oct 2014 12:33:40 -0000

Immediate issue has not cropped up again, but a TITLE uniqueness validator remains...

Phil Charles modified ticket #14

Phil Charles — Thu, 23 Oct 2014 12:33:40 -0000

Discrepancy in search results if line endings are different

Phil Charles modified ticket #5

Phil Charles — Thu, 23 Oct 2014 12:31:14 -0000

Mascot Instrument Config

Phil Charles posted a comment on ticket #50

Phil Charles — Thu, 23 Oct 2014 12:30:32 -0000

Concur. Issue not reported for a few months now.

Phil Charles modified ticket #50

Phil Charles — Thu, 23 Oct 2014 12:30:32 -0000

SINQ Export to Excel Issues

Phil Charles modified ticket #35

Phil Charles — Thu, 23 Oct 2014 12:28:19 -0000

Export mzIdentML

Phil Charles posted a comment on ticket #35

Phil Charles — Thu, 23 Oct 2014 12:28:19 -0000

Some issues remain for generating strictly valid markup (a problem for PRIDE submissions...

Phil Charles committed [6b0666]

Phil Charles — Thu, 23 Oct 2014 12:09:39 -0000

Bugfixes for mzIdentML generator. Markup produ...

Phil Charles committed [51970f]

Phil Charles — Thu, 23 Oct 2014 12:09:39 -0000

Add .snapshot backup dirs to gitignore

Phil Charles committed [b4c5b7]

Phil Charles — Wed, 01 Oct 2014 12:42:21 -0000

Tweak the submission search box to enable searc...

Phil Charles committed [97c54a]

Phil Charles — Wed, 24 Sep 2014 15:17:39 -0000

Fix for timeout in very large Excel files (::Di...

Phil Charles committed [11fc67]

Phil Charles — Wed, 24 Sep 2014 15:10:50 -0000

Bugfix for blank ProteinCenter protein results ...

Phil Charles committed [d05a78]

Phil Charles — Fri, 29 Aug 2014 15:30:39 -0000

Merge branch 'utsw' into oxford

Phil Charles committed [da3821]

Phil Charles — Fri, 29 Aug 2014 15:30:39 -0000

Added extension filter to upload.tt2 as FireFox...

David Trudgian committed [9d569e]

David Trudgian — Fri, 15 Aug 2014 19:39:02 -0000

Merge branch 'utsw'

David Trudgian committed [92f5bf]

David Trudgian — Fri, 15 Aug 2014 19:39:02 -0000

Remove completed work package directories to li...

David Trudgian committed [c59594]

David Trudgian — Fri, 15 Aug 2014 19:39:02 -0000

RemoteSLURM scheduler - now working with TACC S...

David Trudgian committed [e0678e]

David Trudgian — Fri, 15 Aug 2014 19:39:02 -0000

Updating README

David Trudgian committed [7a6ac5]

David Trudgian — Fri, 15 Aug 2014 19:39:02 -0000

Merge branch 'utsw'

David Trudgian committed [77e5fe]

David Trudgian — Fri, 15 Aug 2014 19:39:02 -0000

WIP: RemoteSLURM Shepherd to use TACC Stampede ...

David Trudgian committed [690957]

David Trudgian — Fri, 15 Aug 2014 15:40:25 -0000

Fix INSTALL text about creating main cpfp.conf ...

David Trudgian committed [668584]

David Trudgian — Fri, 15 Aug 2014 15:27:10 -0000

Ugly fix for Carp::Heavy site/local version mis...

David Trudgian committed [d252b9]

David Trudgian — Fri, 15 Aug 2014 15:27:10 -0000

Merge branch 'utsw' of proteomics-srv-01.swmed....