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Commits on Jul 29, 2015
@af11-sanger af11-sanger plasmid maps added to qc test result view (work in progress...) 4849d87
Commits on Jul 30, 2015
@PeterFCKeen PeterFCKeen Changes to wge import testing script 2261ff9
@af11-sanger af11-sanger added reads to plasmid viewer 9c1d63b
@af11-sanger af11-sanger moved some plasmid display processing logic out of template toolkit. …
…fixed read overlap display issue
@PeterFCKeen PeterFCKeen Changes made to test to include new hyperlink 65f337b
@PeterFCKeen PeterFCKeen v0.329
Improved genoverse views
0.329     2015-07-22 10:45:33 Europe/London

    Sponsor front page sub-report updated:
    - Added splice_acceptor calls to the frameshift counts
    - het clones make a green project checkpoint
    - failed project always turn red most recent checkpoint
@PeterFCKeen PeterFCKeen v0.330 3dd3b15
@af11-sanger af11-sanger added alignment target regions to plasmid view b439f9a
@tg6 tg6 Added Het Summary report 3ef1f3a
@tg6 tg6 Merge branch 'devel' of into devel c0ed4ea
@af11-sanger af11-sanger moved plasmid view related logic into Util module e73867d
Commits on Jul 31, 2015
@tg6 tg6 cleanup of test 1a63b6e
@tg6 tg6 added LIMS2_PRIMER_DIR to 0f885bd
Commits on Aug 03, 2015
@af11-sanger af11-sanger do not show plasmid view for es cell qc. catch plasmid view generatio…
…n errors
@af11-sanger af11-sanger added help link describing example plasmid view 45e0bd9
@af11-sanger af11-sanger Merge branch 'devel' into plasmid_viewer 48deb40
Commits on Aug 04, 2015
@af11-sanger af11-sanger added assembly QC verified column to plate report. it is updated on t…
…he fly using js. cannot get the same to work in extjs version of report
Commits on Aug 05, 2015
@af11-sanger af11-sanger update QC verified value in assembly plate view extjs grid b1e223a
@af11-sanger af11-sanger update extjs record with new qc verified vlue 464abef
@af11-sanger af11-sanger stop uninitialized value warning b390009
@af11-sanger af11-sanger Merge branch 'devel' 62ac10a
@af11-sanger af11-sanger v0.331
   Het summary report added
   Vector QC plasmid maps added to result view
   Assembly plate QC verified status flag added
Commits on Aug 06, 2015
@tg6 tg6 added pcr_done to HetSummary report b636144
@tg6 tg6 fixed broken link. uniformization of buttons 5f83140
@tg6 tg6 cached sponsor sub reports now wide e7c07c3
Commits on Aug 10, 2015
@PeterFCKeen PeterFCKeen Merge branch 'devel' f54f1e8
@PeterFCKeen PeterFCKeen Removed debugging tool from script 7ac8619
@PeterFCKeen PeterFCKeen v0.332 8ca30ab
Commits on Aug 11, 2015
@af11-sanger af11-sanger added some extra methods to check region around primers fc1b04c
@af11-sanger af11-sanger pass file server URL to ListLatestRuns module db85a29
Commits on Aug 12, 2015
@af11-sanger af11-sanger fetch error files via file server api 208e283
@tg6 tg6 updated wide front page cached reports c5c3187
@tg6 tg6 Merge branch 'devel' of into devel 2595658
@tg6 tg6 Merge branch 'devel' 71176c3
@tg6 tg6 v0.332
    Front page report wide view update
    Extra methods to check region around primers
@tg6 tg6 v0.333
    Front page report wide view update
    Extra methods to check region around primers
@af11-sanger af11-sanger use new env variable to specify lustre primer dir if running primer g…
…eneration on farm
Commits on Aug 13, 2015
@af11-sanger af11-sanger use the same BWA ref genomes as HTGT QC Util 417a818
Commits on Aug 19, 2015
@af11-sanger af11-sanger always run primer generation locally instead of using farm c73023b
@tg6 tg6 removed Switch feature usage from 370fe56
Commits on Aug 20, 2015
@tg6 tg6 sponsor sub report: het counts are now empty when no pcr has been che…
…cked in
Commits on Aug 21, 2015
@PeterFCKeen PeterFCKeen Added search crisprs by sequence and validation tags to public reports b5d425d
@PeterFCKeen PeterFCKeen Merge branch 'master' of 479d9fb
@PeterFCKeen PeterFCKeen v0.334
    Search crisprs by sequence feature added
    Crispr primer validation checks added to public reports
@tg6 tg6 CrisprPlateOrderSheet updated to show other wells using the crispr afc07fe
@tg6 tg6 Merge branch 'master' into devel d9413d6
@tg6 tg6 small improvements to Search crisprs by sequence f6f6acd
Commits on Aug 24, 2015
@tg6 tg6 design_target_gene_search default crispr type changed to group 9a5bf07
Commits on Aug 25, 2015
@PeterFCKeen PeterFCKeen Fixed bug in public reports 0b736af
@PeterFCKeen PeterFCKeen Merge branch 'peter' into devel 5cddd87
Commits on Aug 26, 2015
@PeterFCKeen PeterFCKeen v0.335
    Fixed bug in the public reports
Commits on Aug 27, 2015
@af11-sanger af11-sanger added interface to create point mutation design from user supplied co…
…ords and sequence
@af11-sanger af11-sanger new design type and oligo type for point mutation designs 7f24abf
Commits on Sep 01, 2015
@af11-sanger af11-sanger trailing space tidy up 44d9bdd
@af11-sanger af11-sanger catch error if traceserver is down and log to console 2507418
Commits on Sep 02, 2015
@af11-sanger af11-sanger show additional environment variables ecde340
@af11-sanger af11-sanger delete fixture data from plate crispr appends e69b724
@af11-sanger af11-sanger workflow change so FP can be frozen back to a single PIQ QC well and …
…fruther FP wells created from this
Commits on Sep 03, 2015
@af11-sanger af11-sanger Merge branch 'devel' into no_lustre dab504d
@af11-sanger af11-sanger perlcritic and test fixes 745e089
@af11-sanger af11-sanger Merge branch 'devel' da80027
@af11-sanger af11-sanger v0.336
    Removed dependancy on lustre file system
    Added point mutation design creation form
    Workflow changes to allow freeze back of Kolf cells to FP
Commits on Sep 07, 2015
@PeterFCKeen PeterFCKeen Added Create Design Plate feature f9041ef
Commits on Sep 08, 2015
@PeterFCKeen PeterFCKeen Create design plate testing, fixtures failing f66e439
@af11-sanger af11-sanger add missing cell line to reference data fixtures e3fe96a
@PeterFCKeen PeterFCKeen Fixed create design plate test d791c30
@dparrysmith dparrysmith Merge branch 'devel' into peter eb8f8ad
@PeterFCKeen PeterFCKeen Merge branch 'devel' of into devel 2399e00
@PeterFCKeen PeterFCKeen Merge branch 'devel' into peter 8e4c1f4
@dparrysmith dparrysmith David's change 7914bc3
@PeterFCKeen PeterFCKeen Merge branch 'peter' of into peter 3c61386
Commits on Sep 09, 2015
@PeterFCKeen PeterFCKeen Changes made 40a54d0
Commits on Sep 10, 2015
@af11-sanger af11-sanger Merge branch 'master' into devel 7b14649
@af11-sanger af11-sanger Merge branch 'devel' of into devel fe84fc6
@PeterFCKeen PeterFCKeen Merge branch 'master' into devel 6dbb790
@af11-sanger af11-sanger Merge branch 'devel' of into devel c7d3bf5
@PeterFCKeen PeterFCKeen Added fixtures and fixed bugs 59aac84
Commits on Sep 15, 2015
@tg6 tg6 Added chromosome and is_het to mutation_signatures_info JSON request 671f454
Commits on Sep 17, 2015
@PeterFCKeen PeterFCKeen Added create crispr and design plate pages and tests a00b28d
@tg6 tg6 Updated summary generation to include experiments. Front page report …
…updated to support experiments and genes with effort concluded now are grey instead of red.
@PeterFCKeen PeterFCKeen Merge branch 'peter' into devel 777b56d
@PeterFCKeen PeterFCKeen Added to Changes ca3166d
@PeterFCKeen PeterFCKeen v0.337
    Added create design and crispr plates function
    Added experiments to summarys table
Commits on Sep 18, 2015
@tg6 tg6 Added experiment_id to front page reports 6a2cc39
Commits on Sep 21, 2015
@tg6 tg6 Sticky table headers when scrolling on front page report ec8a1fd
Commits on Sep 22, 2015
@af11-sanger af11-sanger Merge branch 'devel' into view_traces_manousos 9952ea2
Commits on Sep 23, 2015
@af11-sanger af11-sanger can now get entire trace in traceviewer by not providing search_seq 2f292c6
@af11-sanger af11-sanger get fileserver api url from environment rather than config file a4015a0
Commits on Sep 24, 2015
@af11-sanger af11-sanger added sequence selection functionality (currently only writing to con…
Commits on Sep 28, 2015
@af11-sanger af11-sanger moved genoverse sequence select implementation to WebApp-Common genov…
Commits on Sep 29, 2015
@af11-sanger af11-sanger experiments now linked to gene rather than project c9baafa
Commits on Sep 30, 2015
@af11-sanger af11-sanger added cell lines to projects and modified project view/create bf5717c
@af11-sanger af11-sanger added electroporation cell line to sponsor sub reports 7eda3a8
Commits on Oct 01, 2015
@af11-sanger af11-sanger added some project cell line tests 828df87
@af11-sanger af11-sanger perlcritic fix ab3bae1
@af11-sanger af11-sanger Merge branch 'devel' 89e7874
@af11-sanger af11-sanger v0.339
    Cell line added to projects
    Experiments linked to genes rather than projects
Commits on Oct 02, 2015
@PeterFCKeen PeterFCKeen Incomplete sequencing project 8f37518
Commits on Oct 05, 2015
@PeterFCKeen PeterFCKeen Seq project creation b1512e5
@PeterFCKeen PeterFCKeen Added view seq project page dfcbfd2
@tg6 tg6 Added 'Not to Report' information on the gene page, clone sequencing …
…information section
Commits on Oct 06, 2015
@af11-sanger af11-sanger added util and lims2 API to query redmine for issues by lims2 project id b77a1bf
Commits on Oct 07, 2015
@PeterFCKeen PeterFCKeen Added create and view sequencing projects a6269b7
@PeterFCKeen PeterFCKeen Merge conflict fix 05317dc
@PeterFCKeen PeterFCKeen Merge branch 'master' into devel 0f994a9
@PeterFCKeen PeterFCKeen Perlcritic fix 1526ee4
@af11-sanger af11-sanger added button to create redmine issue for project (contains some FIXMEs) 55245c1
@PeterFCKeen PeterFCKeen v0.340
    Sequencing project 96 plate creation added
    Download sequencing project xlsx added
    Sequencing project view and create interfaces added
Commits on Oct 08, 2015
@af11-sanger af11-sanger only show redmine tracker options to users with sanger email address 4ce01e0
@af11-sanger af11-sanger Merge branch 'devel' into view_traces_manousos b15dba1
@PeterFCKeen PeterFCKeen Changes made to data migration script d89ba42
@af11-sanger af11-sanger new view_traces page to show reads and traces from any seq project (w…
…ork in progress)
@PeterFCKeen PeterFCKeen Added sequencing project tables to fixtures file ce9c5fb
@af11-sanger af11-sanger now displaying read names and showing traces for sub-project 2d585b7
@PeterFCKeen PeterFCKeen Added LIMS2-TEMP 04c2f11
@af11-sanger af11-sanger now with sequence 59e0a43
@tg6 tg6 updated generic_report_grid to link design, gene and crispr ids to th…
…e apropriate pages
@PeterFCKeen PeterFCKeen v0.341 58fecf0
@tg6 tg6 took out front page report sticky headers, cached reports dont like i…
@af11-sanger af11-sanger parse fasta using Bio::SeqIO instead of dodgy regexp 2d5f52c
@af11-sanger af11-sanger added view traces page to nav menu d49c65e
@af11-sanger af11-sanger Merge branch 'devel' into view_traces_manousos 47d1a4d
@PeterFCKeen PeterFCKeen Merge branch 'devel' of into devel 01951c1
@PeterFCKeen PeterFCKeen Env variable updated 5ce367a
Commits on Oct 09, 2015
@PeterFCKeen PeterFCKeen Merge conflict fix f00ec87
@PeterFCKeen PeterFCKeen v0.342 f81368d
@tg6 tg6 Added plate link on es_qc_runs page 54a70b0
Commits on Oct 12, 2015
@af11-sanger af11-sanger Merge branch 'devel' into view_traces_manousos 5a5ca72
@tg6 tg6 create_template_plate interface changed to allow drop down selections…
… when uploading from csv
@tg6 tg6 Merge branch 'devel' of into devel 9b45433
@af11-sanger af11-sanger added script to extract seq data downloaded from Eurofins. more chang…
…es to seq data view page
@af11-sanger af11-sanger Merge branch 'devel' of into devel 1984c58
@af11-sanger af11-sanger Merge branch 'devel' f70db9a
@af11-sanger af11-sanger v0.343
    Added page to view sequence data traces
@tg6 tg6 fixed bug in the gene summary when displaying the not to report flag 4a9c2d2
@tg6 tg6 Merge branch 'devel' of into devel 7760357
Commits on Oct 13, 2015
@af11-sanger af11-sanger import unclipped reads from eurofins. fix primer naming (temp - will …
…be corrected in future submissions)
@af11-sanger af11-sanger Merge branch 'devel' of into devel c3ea436
@af11-sanger af11-sanger resolved merge conflict 9fc96fd
@tg6 tg6 second try in getting the stickyTableHeaders working on the front pag…
…e reports
@tg6 tg6 Merge branch 'devel' of into devel 754036e
@af11-sanger af11-sanger redmine issues not created for an experiment within a project e276596
@af11-sanger af11-sanger Merge branch 'devel' ba82dfa
@tg6 tg6 front page reports sticky headers removed, need to test first without 7ba0c1e
@tg6 tg6 Merge branch 'devel' of into devel 82856e2
@af11-sanger af11-sanger v0.344
   Added view and create links from project/experiment view to redmine
Commits on Oct 14, 2015
@tg6 tg6 Added pagination to crisprqc/es_qc_runs page 006d2b9
@tg6 tg6 Merge branch 'master' into devel 19f45d6
Commits on Oct 15, 2015
@PeterFCKeen PeterFCKeen 384 plates 600adc7
@PeterFCKeen PeterFCKeen Seq_proj search and 384 plates implemented 5881e3f
@PeterFCKeen PeterFCKeen Changes made for perlcritic 9a2d4e3
@af11-sanger af11-sanger primer count data now restored after viewing reads for subproject ec9fd96
@af11-sanger af11-sanger Merge branch 'devel' of into devel 78248d6
@PeterFCKeen PeterFCKeen added sequencing project tables to the test and fixtures modules 7dd1efe
@PeterFCKeen PeterFCKeen Merge branch 'peter' into devel 213d3d4
@PeterFCKeen PeterFCKeen Uncommited changes c95919e
@af11-sanger af11-sanger include project priority in redmine ticket creation dc2b829
Commits on Oct 16, 2015
@PeterFCKeen PeterFCKeen v0.345 f50bb19
Commits on Oct 19, 2015
@af11-sanger af11-sanger highlight read sequence visible in traceviewer plot 3dff070
@af11-sanger af11-sanger show peak height scale in traceviewer 2020e70
@af11-sanger af11-sanger Merge branch 'devel' 8fd7a73
@af11-sanger af11-sanger v0.346
  Sequence highlighting on trace view page
Commits on Oct 20, 2015
@af11-sanger af11-sanger traceview linked to sequence highlighting in crispr QC results" cfd2ea4
@af11-sanger af11-sanger extra border lines within read region removed bff56ca
@af11-sanger af11-sanger remove highlighting on hide traces and if visible read is not found i…
…n sequence
@af11-sanger af11-sanger user redirected to requested page after login 887a051
@af11-sanger af11-sanger bugfix: show species from crispr group, not session 0b3003e
@tg6 tg6 not to report flag added to Electroporation stage on the gene summary…
… page
@tg6 tg6 Merge branch 'devel' of into devel fa07669
Commits on Oct 21, 2015
@af11-sanger af11-sanger download seq project reads as fasta d37e180
@tg6 tg6 Added seach capabilities to /user/crisprqc/es_qc_runs crispr_es_qc page bc84dc4
@tg6 tg6 Merge branch 'devel' of into devel d05c4ef
Commits on Oct 22, 2015
@PeterFCKeen PeterFCKeen Added accordions and search functionality to the mutation signatures …
@PeterFCKeen PeterFCKeen Merge branch 'devel' of into devel 1981277
@PeterFCKeen PeterFCKeen Merge branch 'peter' into devel c8b04f8
@af11-sanger af11-sanger Merge branch 'devel' c3b61d5
@af11-sanger af11-sanger perlcritic fix 5e31560
@af11-sanger af11-sanger v0.347
  Gene symbols and searching added to mutation signatures barcodes page
  Sequence highlighting added to crispr QC view page
Commits on Oct 23, 2015
@tg6 tg6 Fixed bug in crispr_es_qc runs seach 13f587f
@tg6 tg6 Merge branch 'devel' of into devel 8747f7a
@tg6 tg6 v0.348
    Search updated in CRISPR QC Runs
    is_het added to mutation signatures JSON string
@dparrysmith dparrysmith First readme file 6a9bbe1
@dparrysmith dparrysmith Update 847faeb
@dparrysmith dparrysmith Update 354471b
@dparrysmith dparrysmith Update f3c28da
@dparrysmith dparrysmith Merge branch 'devel' into david_misc e4f231d
@dparrysmith dparrysmith Added process graph example image 33ffa6b
@dparrysmith dparrysmith Readme changes f950c28
@dparrysmith dparrysmith Update b6b46a5
@dparrysmith dparrysmith Added process_graph example image 843c157
Commits on Oct 26, 2015
@PeterFCKeen PeterFCKeen Fixed bug in SeqProj and added XLSX download option to reports dffe0b5
@PeterFCKeen PeterFCKeen Merge branch 'devel' into peter c501030
@PeterFCKeen PeterFCKeen Added accordion search to gene summary 3853aa1
@PeterFCKeen PeterFCKeen perlcritic fix 5781da3
@PeterFCKeen PeterFCKeen Merge branch 'devel' c464cdd
@PeterFCKeen PeterFCKeen Perlcritic fix 11c6341
@PeterFCKeen PeterFCKeen v0.349
    Added highlight search to gene summary
    Added XLSX download to reports
Commits on Oct 27, 2015
@af11-sanger af11-sanger refactored sequencing data extraction into module in preparation to a…
…utomate using sFTP
@af11-sanger af11-sanger some regex fixing 50809f3
Commits on Oct 28, 2015
@tg6 tg6 Crispr QC Run deletion allowed by cascading foreign key constraint to…
… crispr_validation
Commits on Nov 03, 2015
@af11-sanger af11-sanger data download from FTPS site now handled by lftp instead of perl c810f4d
@af11-sanger af11-sanger Merge branch 'devel' into eurofins 575a7bc
@af11-sanger af11-sanger perlcritic fix 0f28294
@af11-sanger af11-sanger moved seq data extract script to scripts so it gets deployed cd8d27f
@af11-sanger af11-sanger v0.350
    Improvements to Eurofins data extraction script
Commits on Nov 04, 2015
@af11-sanger af11-sanger detect if click is in oligo of gibson design and display oligo info 5adfd7a
@tg6 tg6 refactoring of 6e51e72
@tg6 tg6 Merge branch 'master' into devel fd015ea
Commits on Nov 05, 2015
@tg6 tg6 generic grid urls modified to open in a new page 480f83e
@af11-sanger af11-sanger show selected region size in genoverse c9b1c11
@af11-sanger af11-sanger Merge branch 'devel' of into devel d113aa6
Commits on Nov 06, 2015
@PeterFCKeen PeterFCKeen Unfinished changes to create design d6379cf
@tg6 tg6 CRISPR plate grid report truncation fixed. Added WGE Crispr ID. Fixed…
… report CSV download.
@tg6 tg6 Fixed bug in 5266780
@tg6 tg6 removed debug statement 330d32f
@tg6 tg6 v0.351
    Bugfixes to the generic grid report
@tg6 tg6 Merge branch 'devel' 9eadcf3
Commits on Nov 07, 2015
@tg6 tg6 v0.352 3d6fecd
Commits on Nov 09, 2015
@af11-sanger af11-sanger fixed seq data import bug affecting empty well files 0de888a
@af11-sanger af11-sanger added help text to sequencing project pages 64d34c5
Commits on Nov 10, 2015
@PeterFCKeen PeterFCKeen redunant changes c6e95b1
@af11-sanger af11-sanger v0.353
  Bug fix to sequencing import. Added sequencing project help text
@PeterFCKeen PeterFCKeen minor changes e6691f8
Commits on Nov 11, 2015
@PeterFCKeen PeterFCKeen reverted changes to design info bef46d7
@PeterFCKeen PeterFCKeen Merge branch 'seq_proj' into peter 80a41c4
Commits on Nov 12, 2015
@tg6 tg6 crispr search species check added and redirect fixed ec62ab2
Commits on Nov 20, 2015
@tg6 tg6 front page report het display dash when not done 2883763
Commits on Nov 24, 2015
@tg6 tg6 front page report warning cleanup dc4bf00
Commits on Nov 26, 2015
@tg6 tg6 species switch now stays on same page instead of homepage 21ed31c
@tg6 tg6 bugfix on crispr qc, checking if a well is accepted on any run c449378
@tg6 tg6 numerical comparison replaced by boolean check 2c35cf4
@PeterFCKeen PeterFCKeen Fusion changes for database 7024f58
@PeterFCKeen PeterFCKeen Database and appends changes b9fbb9b
@PeterFCKeen PeterFCKeen Added audit file 693dde2
Commits on Nov 27, 2015
@tg6 tg6 Refactoring of gene summary page. Update of Electroporation section ece4d6d
@tg6 tg6 Added het status to Gene Summary cbb2098
@tg6 tg6 Updated tests for Gene plugin 732709e
@tg6 tg6 updated to replace deprecated search_genes method 1318419
Commits on Nov 30, 2015
@tg6 tg6 model dump schema f252fa1
@tg6 tg6 gene summary test issues fixed ed76ab6
@tg6 tg6 Merge branch 'devel' of into devel e9ee1f1
@tg6 tg6 Merge branch 'devel' 1f502e6
@tg6 tg6 v0.354
    bugfix on crispr qc, checking if a well is accepted on any run
    species switch now stays on same page instead of homepage
    gene summary page: added het status, update to electroporation section, refactoring to speed up
    front page report warnings cleanup
    search_genes method deprecated
Commits on Dec 01, 2015
@PeterFCKeen PeterFCKeen merge conflicts 4c7eea9
@PeterFCKeen PeterFCKeen Merge branch 'master' into peter 74459c7
@PeterFCKeen PeterFCKeen Merge branch 'devel' of into devel 5b71241
@PeterFCKeen PeterFCKeen conflict resolve 37fea78
@PeterFCKeen PeterFCKeen Perlcritic issues 957c3b3
@PeterFCKeen PeterFCKeen v0.354
    Changes made for Fusion-Deletion
    Initial release for testing on staging
@PeterFCKeen PeterFCKeen v0.355 b350c88