Activity for jinman

  • jinman jinman committed [r53]

    MODIFIED: VIGOR3.pm - modified blast+ calls to have new minimum wordsize of 2, based on blast+ constraints; numerous changes to regexes for parsing blast+ output

  • jinman jinman committed [r52]

    MODIFIED: README.txt - removed references to removed modules, added reference to Config::IniFiles

  • jinman jinman committed [r51]

    database updates

  • jinman jinman committed [r50]

    MODIFIED: numerous changes to allow transition from blast to blast+

  • jinman jinman committed [r164]

    MODIFIED: create_meta_groupings.pl - touched up pod in help documentation for clarity/formatting

  • jinman jinman committed [r163]

    MODIFIED: parse_genbank_files.pl - changed name...

  • jinman jinman committed [r47]

    Converted fastacmd calls to blast+ blastdbcmd

  • jinman jinman committed [r46]

    Migration of formatdb calls to blast+ makeblast...

  • jinman jinman committed [r45]

    Creating branch for jinman to change blast call...

  • jinman jinman committed [r44]

    Added flavors/ to prod3/config

  • jinman jinman committed [r43]

    Added flavors/ to prod3/config

  • jinman jinman committed [r42]

    Added flavors/ to prod3/config

  • jinman jinman committed [r162]

    Revamped printing of genome list file for check...

  • jinman jinman committed [r41]

    Tagging VIGOR3.2

  • jinman jinman committed [r40]

    jinman merge of config .ini changes

  • jinman jinman committed [r39]

    Merged jmiller's changes back into this branch

  • jinman jinman committed [r38]

    Changed default path in runRegressionTests.pl

  • jinman jinman committed [r37]

    removing db.pm as it's no longer needed with sw...

  • jinman jinman committed [r36]

    Changes to VIGOR3.pl and VIGOR3.pm to use .ini ...

  • jinman jinman committed [r35]

    Adding config dir to store .ini files

  • jinman jinman committed [r34]

    Creating branch for jinman's switch from sqlite...

  • jinman jinman committed [r28]

    runRegressionTests.pl - now correctly counts th...

  • jinman jinman committed [r161]

    MODIFIED: ftp_download_ncbi_annotation.pl - imp...

  • jinman jinman committed [r160]

    MODIFIED: parse_genbank_files.pl - slightly bet...

  • jinman jinman committed [r159]

    MODIFIED: parse_genbank_files.pl - now checks t...

  • jinman jinman committed [r158]

    MODIFIED: parse_genbank_files.pl - new option '...

  • jinman jinman committed [r157]

    MODIFIED: ftp_download_ncbi_annotation.pl - now...

  • jinman jinman committed [r156]

    MODIFIED: parse_genbank_files.pl - now calls do...

  • jinman jinman committed [r155]

    MODIFIED: ftp_download_ncbi_annotation.pl - now...

  • jinman jinman committed [r154]

    MODIFIED: ftp_download_ncbi_annotation.pl - no ...

  • jinman jinman committed [r153]

    MODIFIED: ftp_download_ncbi_annotation.pl - now...

  • jinman jinman committed [r152]

    MODIFIED: ftp_download_ncbi_annotation.pl - fix...

  • jinman jinman committed [r151]

    MODIFIED: runPangenome.pl - corrected path to $...

  • jinman jinman committed [r150]

    MODIFIED: bin/make_BSR_trees.sh, bin/Newick-rub...

  • jinman jinman committed [r149]

    MODIFIED: run_iterative_pangenome.pl - switched...

  • jinman jinman committed [r148]

    ADDED: get_collection_date.pl - create a list o...

  • jinman jinman committed [r146]

    MODIFIED: run_iterative_pangenome.pl, runPangen...

  • jinman jinman committed [r145]

    MODIFIED: parse_genbank_files.pl - now attempts...

  • jinman jinman committed [r144]

    MODIFIED: run_iterative_pangenome.pl - now flus...

  • jinman jinman committed [r143]

    MODIFIED: runPangenome.pl, run_iterative_pangen...

  • jinman jinman committed [r140]

    MODIFIED: run_iterative_pangenome.pl - changed ...

  • jinman jinman committed [r139]

    MODIFIED: run_iterative_pangenome.pl - changed ...

  • jinman jinman committed [r138]

    MODIFIED: ftp_download_ncbi_annotation.pl - (1)...

  • jinman jinman committed [r137]

    MODIFIED: run_iterative_pangenome.pl - 1. optio...

  • jinman jinman committed [r136]

    MODIFIED: run_iterative_pangenome.pl - added --...

  • jinman jinman committed [r135]

    MODIFIED: check_att_files.pl - fixed bug encodi...

  • jinman jinman committed [r133]

    MODIFIED: ftp_download_ncbi_annotation.pl - imp...

  • jinman jinman committed [r132]

    MODIFIED: check_att_files.pl - better descripti...

  • jinman jinman committed [r130]

    MODIFIED: runPangenome.pl - moves core_cluster_...

  • jinman jinman committed [r129]

    MODIFIED: runPangenome.pl - now uses blast+! A...

  • jinman jinman committed [r128]

    MODIFIED: run_iterative_pangenome.pl - changed ...

  • jinman jinman committed [r127]

    MODIFIED: run_iterative_pangenome.pl - minor ch...

  • jinman jinman committed [r125]

    MODIFIED: pan_chromosome scripts have been upda...

  • jinman jinman committed [r124]

    MODIFIED: runPangenome.pl - more graphics scripts.

  • jinman jinman committed [r123]

    MODIFIED: ftp_download_ncbi_annotation.pl - now...

  • jinman jinman committed [r120]

    MODIFIED: gene_order.pl, ftp_download_ncbi_anno...

  • jinman jinman committed [r119]

    MODIFIED: runPangenome.pl, pan_chromosome/graph...

  • jinman jinman committed [r118]

    ADDED: core_cluster_histogram.R

  • jinman jinman committed [r117]

    ADDED: pan_chromosome; MODIFIED: runPangenome.p...

  • jinman jinman committed [r116]

    MODIFIED: ftp_download_ncbi_annotation.pl - add...

  • jinman jinman committed [r115]

    MODIFIED: run_iterative_pangenome.pl - added --...

  • jinman jinman committed [r114]

    MODIFIED: ftp_download_ncbi_annotation.pl - tri...

  • jinman jinman committed [r113]

    MODIFIED: check_att_files.pl - now automaticall...

  • jinman jinman committed [r112]

    MODIFIED: ftp_download_ncbi_annotation.pl - new...

  • jinman jinman committed [r111]

    MODIFIED: run_iterative_pangenome.pl - now copi...

  • jinman jinman committed [r110]

    ADDED: check_att_files.pl - examine att_files t...

  • jinman jinman committed [r109]

    MODIFIED: ftp_download_ncbi_annotation.pl - now...

  • jinman jinman committed [r108]

    MODIFIED: run_iterative_pangenome.pl - centroid...

  • jinman jinman committed [r107]

    MODIFIED: run_iterative_pangenome.pl - now runs...

  • jinman jinman committed [r106]

    MODIFIED: ftp_download_ncbi_annotation.pl - add...

  • jinman jinman committed [r105]

    MODIFIED: ftp_download_ncbi_annotation.pl - new...

  • jinman jinman committed [r104]

    MODIFIED: ftp_download_ncbi_annotation.pl - cha...

  • jinman jinman committed [r103]

    MODIFIED: ftp_download_ncbi_annotation.pl - add...

  • jinman jinman committed [r102]

    MODIFIED: ftp_download_ncbi_annotation - now ac...

  • jinman jinman committed [r101]

    MODIFIED: download_ncbi_annotation.pl - revised...

  • jinman jinman committed [r100]

    MODIFIED: parse_genbank_files.pl - improved han...

  • jinman jinman committed [r99]

    MODIFIED: gene_order.pl - moved print_index cal...

  • jinman jinman committed [r98]

    MODIFIED: bin/ftp_download_ncbi_annotation.pl -...

  • jinman jinman committed [r97]

    MODIFIED: bin/ftp_download_ncbi_annotation.pl -...

  • jinman jinman committed [r96]

    MODIFIED: bin/ftp_download_ncbi_annotation.pl -...

  • jinman jinman committed [r95]

    MODIFIED: bin/ftp_download_ncbi_annotation.pl -...

  • jinman jinman committed [r94]

    MODIFIED: bin/ftp_download_ncbi_annotation.pl -...

  • jinman jinman committed [r93]

    MODIFIED: bin/ftp_download_ncbi_annotation.pl -...

  • jinman jinman committed [r92]

    MODIFIED: bin/ftp_download_ncbi_annotation.pl -...

  • jinman jinman committed [r91]

    MODIFIED: bin/ftp_download_ncbi_annotation.pl -...

  • jinman jinman committed [r90]

    MODIFIED: bin/ftp_download_ncbi_annotation.pl -...

  • jinman jinman committed [r89]

    ADDED: bin/ftp_download_ncbi_annotation.pl - In...

  • jinman jinman committed [r85]

    MODIFIED: bin/runPangenome.pl - revamped params...

  • jinman jinman committed [r83]

    ADDED: lib/TIGR/FASTAgrammar.pm; MODIFIED: bin/...

  • jinman jinman committed [r82]

    MODIFIED: download_ncbi_annotation.pl - updated...

  • jinman jinman committed [r78]

    MODIFIED: parse_genbank_file.pl, runPangenome.p...

  • jinman jinman committed [r75]

    MODIFIED: run_iterative_pangenome.pl - no longe...

  • jinman jinman committed [r74]

    MODIFIED: run_iterative_pangenome.pl - removed ...

  • jinman jinman committed [r72]

    MODIFIED: runPangenome.pl - whitespace and inde...

  • jinman jinman committed [r71]

    MODIFIED: run_iterative_pangenome.pl - added gr...

  • jinman jinman committed [r70]

    Modified: bin/parse_genbank_files.pl - better c...

  • jinman jinman committed [r69]

    Forgot to commit tree-making scripts. doh.

  • jinman jinman committed [r68]

    Many additional scripts and a few ruby libs to ...

  • jinman jinman committed [r67]

    MODIFIED: bin/download_ncbi_annotation.pl - now...

  • jinman jinman committed [r66]

    MODIFIED: bin/download_ncbi_annotation.pl - now...

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