Mercurial > repos > galaxyp > peptideshaker

comparison galaxyp-toolshed-peptideshaker @ 1:7a74818e0eeb draft

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Improved some datatype handling
author galaxyp
date Thu, 20 Jun 2013 10:53:16 -0400
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0:0578e296cab4 1:7a74818e0eeb
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471 <section id="readme">
472
473 <article class="readme file">
474 <p>Tool wrapper for SearchGUI + PeptideShaker. This tool takes any number
475 of mgf files and performs X! Tandem and OMSSA searches on these via
476 SearchGUI and merges the results using PeptideShaker.</p>
477 <p>For Galaxy-P we are installing this tool via CloudBioLinux
478 (https://github.com/jmchilton/cloudbiolinux/blob/proteomics/cloudbio/custom/bio_proteomics.py). While
479 this fabric script may not be exactly appropriate for your environment
480 it may serve as a template for how to install this software. In
481 particular these tools require CLI wrappers to be placed for
482 PeptideShaker and SearchGUI that can be installed as demostrated in
483 these fabric functions.</p>
484 <p>Note: Also SearchGUI requires a version greater than 1.12.2 which
485 contained several bugs preventing this from working on the
486 command-line and via Linux.</p>
487 <p>Also, PeptideShaker may require xvfb to simulate an X environment if
488 this is installed on a headless server.</p>
489 <h1 id="markdown-header-obtaining-tools">Obtaining Tools</h1>
490 <p>Repositories for all Galaxy-P tools can be found at
491 https:/bitbucket.org/galaxyp/.</p>
492 <h1 id="markdown-header-contact">Contact</h1>
493 <p>Please send suggestions for improvements and bug reports to
494 jmchilton@gmail.com.</p>
495 <h1 id="markdown-header-license">License</h1>
496 <p>All Galaxy-P tools are licensed under the Apache License Version 2.0
497 unless otherwise documented.</p>
498 <h1 id="markdown-header-tool-versioning">Tool Versioning</h1>
499 <p>Galaxy-P tools will have versions of the form X.Y.Z. Versions
500 differing only after the second decimal should be completely
501 compatible with each other. Breaking changes should result in an
502 increment of the number before and/or after the first decimal. All
503 tools of version less than 1.0.0 should be considered beta.</p>
504 </article>
505
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512 Recent activity
513 <a href="/galaxyp/galaxyp-toolshed-peptideshaker/rss" class="icon rss">RSS feed fo galaxyp-toolshed-peptideshaker</a>
514 </h1>
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541 <a href="/galaxyp"><img alt="galaxyp" src="https://secure.gravatar.com/avatar/655358b258b3fbd64aa5c6f42adade4e?d=https%3A%2F%2Fd3oaxc4q5k2d6q.cloudfront.net%2Fm%2F968d9745b7be%2Fimg%2Fdefault_team_avatar%2F32%2Fteam_blue.png&amp;s=32" class="avatar avatar32" /></a>
542
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544 <p>
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547 <a href="/galaxyp">galaxyp</a>
548
549 pushed 1 commit to
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552 <a href="/galaxyp/galaxyp-toolshed-peptideshaker" title="galaxyp/galaxyp-toolshed-peptideshaker">galaxyp/galaxyp-toolshed-peptideshaker</a>
553
554
555 </p>
556 <time datetime="2013-06-19T22:19:56+00:00">16 hours ago</time>
557
558 <div class="changeset">
559 <a href="/galaxyp/galaxyp-toolshed-peptideshaker/commits/80ef7cf0d97a14a59b39f2d7eb683531cc02056a" class="changeset-hash">80ef7cf</a>
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563 improved some datatypes
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592 <article class="news-item commit">
593 <span class="icon commit"></span>
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597 <a href="/jmchilton"><img alt="John Chilton" src="https://secure.gravatar.com/avatar/86cbb595c758989c14ae715c44588998?d=https%3A%2F%2Fd3oaxc4q5k2d6q.cloudfront.net%2Fm%2F968d9745b7be%2Fimg%2Fdefault_avatar%2F32%2Fuser_blue.png&amp;s=32" class="avatar avatar32" /></a>
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600 <p>
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603 <a href="/jmchilton">John Chilton</a>
604
605 pushed 1 commit to
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608 <a href="/galaxyp/galaxyp-toolshed-peptideshaker" title="galaxyp/galaxyp-toolshed-peptideshaker">galaxyp/galaxyp-toolshed-peptideshaker</a>
609
610
611 </p>
612 <time datetime="2013-06-07T03:03:07+00:00">2013-06-07</time>
613
614 <div class="changeset">
615 <a href="/galaxyp/galaxyp-toolshed-peptideshaker/commits/113acce8b7eea4ed179411f6704ab5a5d8245da8" class="changeset-hash">113acce</a>
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619 Ensure unique Experiment/Sample names. Peptideshaker seems to potentially have clean up problem on errors otherwise.
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649 <a href="/jmchilton"><img alt="John Chilton" src="https://secure.gravatar.com/avatar/86cbb595c758989c14ae715c44588998?d=https%3A%2F%2Fd3oaxc4q5k2d6q.cloudfront.net%2Fm%2F968d9745b7be%2Fimg%2Fdefault_avatar%2F32%2Fuser_blue.png&amp;s=32" class="avatar avatar32" /></a>
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652 <p>
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655 <a href="/jmchilton">John Chilton</a>
656
657 pushed 1 commit to
658
659
660 <a href="/galaxyp/galaxyp-toolshed-peptideshaker" title="galaxyp/galaxyp-toolshed-peptideshaker">galaxyp/galaxyp-toolshed-peptideshaker</a>
661
662
663 </p>
664 <time datetime="2013-05-20T15:26:48+00:00">2013-05-20</time>
665
666 <div class="changeset">
667 <a href="/galaxyp/galaxyp-toolshed-peptideshaker/commits/6fa4a7ad242f1ce78db6eaec19099bd1b7f86b2f" class="changeset-hash">6fa4a7a</a>
668 -
669
670
671 Add script to create a target-decoy database for PeptideShaker - seems very picky about the format of the database.
672
673
674 </div>
675
676
677 </article>
678
679
680
681
682
683
684
685
686
687
688
689
690
691
692
693
694
695
696 <article class="news-item commit">
697 <span class="icon commit"></span>
698
699
700
701 <a href="/jmchilton"><img alt="John Chilton" src="https://secure.gravatar.com/avatar/86cbb595c758989c14ae715c44588998?d=https%3A%2F%2Fd3oaxc4q5k2d6q.cloudfront.net%2Fm%2F968d9745b7be%2Fimg%2Fdefault_avatar%2F32%2Fuser_blue.png&amp;s=32" class="avatar avatar32" /></a>
702
703
704 <p>
705
706
707 <a href="/jmchilton">John Chilton</a>
708
709 pushed 2 commits to
710
711
712 <a href="/galaxyp/galaxyp-toolshed-peptideshaker" title="galaxyp/galaxyp-toolshed-peptideshaker">galaxyp/galaxyp-toolshed-peptideshaker</a>
713
714
715 </p>
716 <time datetime="2013-05-13T18:51:02+00:00">2013-05-13</time>
717
718 <div class="changeset">
719 <a href="/galaxyp/galaxyp-toolshed-peptideshaker/commits/bf3730228118ac8adee5e5fc16f08ad5f9aaaf0e" class="changeset-hash">bf37302</a>
720 -
721
722
723 Add CPS datatype.
724
725
726 </div>
727
728 <div class="changeset">
729 <a href="/galaxyp/galaxyp-toolshed-peptideshaker/commits/d63d2ed28d002156d5330d29afbf8afc54adfc3b" class="changeset-hash">d63d2ed</a>
730 -
731
732
733 Improve documentation.
734
735
736 </div>
737
738
739 </article>
740
741
742
743
744
745
746
747
748
749
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753
754
755
756
757
758 <article class="news-item commit">
759 <span class="icon commit"></span>
760
761
762
763 <a href="/jmchilton"><img alt="John Chilton" src="https://secure.gravatar.com/avatar/86cbb595c758989c14ae715c44588998?d=https%3A%2F%2Fd3oaxc4q5k2d6q.cloudfront.net%2Fm%2F968d9745b7be%2Fimg%2Fdefault_avatar%2F32%2Fuser_blue.png&amp;s=32" class="avatar avatar32" /></a>
764
765
766 <p>
767
768
769 <a href="/jmchilton">John Chilton</a>
770
771 pushed 1 commit to
772
773
774 <a href="/galaxyp/galaxyp-toolshed-peptideshaker" title="galaxyp/galaxyp-toolshed-peptideshaker">galaxyp/galaxyp-toolshed-peptideshaker</a>
775
776
777 </p>
778 <time datetime="2013-05-10T21:39:19+00:00">2013-05-10</time>
779
780 <div class="changeset">
781 <a href="/galaxyp/galaxyp-toolshed-peptideshaker/commits/a76da3b08725332a9dc746b3f4e886d047af2e40" class="changeset-hash">a76da3b</a>
782 -
783
784
785 Add license and documentation.
786
787
788 </div>
789
790
791 </article>
792
793
794
795
796
797
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799
800
801
802
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804
805
806
807
808
809
810 <article class="news-item commit">
811 <span class="icon commit"></span>
812
813
814
815 <a href="/jmchilton"><img alt="John Chilton" src="https://secure.gravatar.com/avatar/86cbb595c758989c14ae715c44588998?d=https%3A%2F%2Fd3oaxc4q5k2d6q.cloudfront.net%2Fm%2F968d9745b7be%2Fimg%2Fdefault_avatar%2F32%2Fuser_blue.png&amp;s=32" class="avatar avatar32" /></a>
816
817
818 <p>
819
820
821 <a href="/jmchilton">John Chilton</a>
822
823 pushed 1 commit to
824
825
826 <a href="/galaxyp/galaxyp-toolshed-peptideshaker" title="galaxyp/galaxyp-toolshed-peptideshaker">galaxyp/galaxyp-toolshed-peptideshaker</a>
827
828
829 </p>
830 <time datetime="2013-05-10T21:33:27+00:00">2013-05-10</time>
831
832 <div class="changeset">
833 <a href="/galaxyp/galaxyp-toolshed-peptideshaker/commits/29ee7c62dfdc24848cc1111500d544c700ca9008" class="changeset-hash">29ee7c6</a>
834 -
835
836
837 Add sample loc file for toolshed.
838
839
840 </div>
841
842
843 </article>
844
845
846
847
848
849
850
851
852
853
854
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856
857
858
859
860
861
862 <article class="news-item commit">
863 <span class="icon commit"></span>
864
865
866
867 <a href="/jmchilton"><img alt="John Chilton" src="https://secure.gravatar.com/avatar/86cbb595c758989c14ae715c44588998?d=https%3A%2F%2Fd3oaxc4q5k2d6q.cloudfront.net%2Fm%2F968d9745b7be%2Fimg%2Fdefault_avatar%2F32%2Fuser_blue.png&amp;s=32" class="avatar avatar32" /></a>
868
869
870 <p>
871
872
873 <a href="/jmchilton">John Chilton</a>
874
875 pushed 1 commit to
876
877
878 <a href="/galaxyp/galaxyp-toolshed-peptideshaker" title="galaxyp/galaxyp-toolshed-peptideshaker">galaxyp/galaxyp-toolshed-peptideshaker</a>
879
880
881 </p>
882 <time datetime="2013-04-12T18:58:24+00:00">2013-04-12</time>
883
884 <div class="changeset">
885 <a href="/galaxyp/galaxyp-toolshed-peptideshaker/commits/8384b7acd805161da0b61203688c61ed0b11b72b" class="changeset-hash">8384b7a</a>
886 -
887
888
889 Fix modification handling.
890
891
892 </div>
893
894
895 </article>
896
897
898
899
900
901
902
903
904
905
906
907
908
909
910
911
912
913
914 <article class="news-item commit">
915 <span class="icon commit"></span>
916
917
918
919 <a href="/jmchilton"><img alt="John Chilton" src="https://secure.gravatar.com/avatar/86cbb595c758989c14ae715c44588998?d=https%3A%2F%2Fd3oaxc4q5k2d6q.cloudfront.net%2Fm%2F968d9745b7be%2Fimg%2Fdefault_avatar%2F32%2Fuser_blue.png&amp;s=32" class="avatar avatar32" /></a>
920
921
922 <p>
923
924
925 <a href="/jmchilton">John Chilton</a>
926
927 pushed 1 commit to
928
929
930 <a href="/galaxyp/galaxyp-toolshed-peptideshaker" title="galaxyp/galaxyp-toolshed-peptideshaker">galaxyp/galaxyp-toolshed-peptideshaker</a>
931
932
933 </p>
934 <time datetime="2013-04-11T18:38:44+00:00">2013-04-11</time>
935
936 <div class="changeset">
937 <a href="/galaxyp/galaxyp-toolshed-peptideshaker/commits/735b677030185833e6dee7a38e37a0b8ef49a2fb" class="changeset-hash">735b677</a>
938 -
939
940
941 PeptideShaker modifications need to be all lower case.
942
943
944 </div>
945
946
947 </article>
948
949
950
951
952
953
954
955
956
957
958
959
960
961
962
963
964
965
966 <article class="news-item commit">
967 <span class="icon commit"></span>
968
969
970
971 <a href="/jmchilton"><img alt="John Chilton" src="https://secure.gravatar.com/avatar/86cbb595c758989c14ae715c44588998?d=https%3A%2F%2Fd3oaxc4q5k2d6q.cloudfront.net%2Fm%2F968d9745b7be%2Fimg%2Fdefault_avatar%2F32%2Fuser_blue.png&amp;s=32" class="avatar avatar32" /></a>
972
973
974 <p>
975
976
977 <a href="/jmchilton">John Chilton</a>
978
979 pushed 2 commits to
980
981
982 <a href="/galaxyp/galaxyp-toolshed-peptideshaker" title="galaxyp/galaxyp-toolshed-peptideshaker">galaxyp/galaxyp-toolshed-peptideshaker</a>
983
984
985 </p>
986 <time datetime="2013-04-08T19:54:06+00:00">2013-04-08</time>
987
988 <div class="changeset">
989 <a href="/galaxyp/galaxyp-toolshed-peptideshaker/commits/1f4e30851033eb83986c2d793ba894604f9fe1b0" class="changeset-hash">1f4e308</a>
990 -
991
992
993 Implement modifications for peptide_shaker wrapper.
994
995
996 </div>
997
998 <div class="changeset">
999 <a href="/galaxyp/galaxyp-toolshed-peptideshaker/commits/90c86636c57d28ba6f369e0e0d1aa097c46f5d4b" class="changeset-hash">90c8663</a>
1000 -
1001
1002
1003 Initial work on building modification list for searchGUI.
1004
1005
1006 </div>
1007
1008
1009 </article>
1010
1011
1012
1013
1014
1015
1016
1017
1018
1019
1020
1021
1022
1023
1024
1025
1026
1027
1028 <article class="news-item commit">
1029 <span class="icon commit"></span>
1030
1031
1032
1033 <a href="/jmchilton"><img alt="John Chilton" src="https://secure.gravatar.com/avatar/86cbb595c758989c14ae715c44588998?d=https%3A%2F%2Fd3oaxc4q5k2d6q.cloudfront.net%2Fm%2F968d9745b7be%2Fimg%2Fdefault_avatar%2F32%2Fuser_blue.png&amp;s=32" class="avatar avatar32" /></a>
1034
1035
1036 <p>
1037
1038
1039 <a href="/jmchilton">John Chilton</a>
1040
1041 pushed 1 commit to
1042
1043
1044 <a href="/galaxyp/galaxyp-toolshed-peptideshaker" title="galaxyp/galaxyp-toolshed-peptideshaker">galaxyp/galaxyp-toolshed-peptideshaker</a>
1045
1046
1047 </p>
1048 <time datetime="2013-03-19T19:23:06+00:00">2013-03-19</time>
1049
1050 <div class="changeset">
1051 <a href="/galaxyp/galaxyp-toolshed-peptideshaker/commits/21b540795f0663a4633a53c78d733746a463167d" class="changeset-hash">21b5407</a>
1052 -
1053
1054
1055 Fix label on protein report.
1056
1057
1058 </div>
1059
1060
1061 </article>
1062
1063
1064
1065
1066
1067
1068 </article>
1069
1070
1071
1072
1073
1074 </div>
1075
1076
1077
1078
1079
1080
1081 </section>
1082 </div>
1083
1084 <div class="column">
1085
1086
1087
1088
1089 <section id="repo-stats">
1090
1091 <div class="clone-url">
1092 <div class="aui-buttons">
1093 <a href="https://bitbucket.org/galaxyp/galaxyp-toolshed-peptideshaker"
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1096 <span class="dropdown-text">HTTPS</span>
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1100 <li>
1101 <a href="https://bitbucket.org/galaxyp/galaxyp-toolshed-peptideshaker"
1102
1103 data-command="https://bitbucket.org/galaxyp/galaxyp-toolshed-peptideshaker"
1104
1105 class="item-link https">HTTPS
1106 </a>
1107 </li>
1108 <li>
1109 <a href="ssh://hg@bitbucket.org/galaxyp/galaxyp-toolshed-peptideshaker"
1110
1111 data-command="ssh://hg@bitbucket.org/galaxyp/galaxyp-toolshed-peptideshaker"
1112
1113 class="item-link ssh">SSH
1114 </a>
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1118 <input type="text" readonly="readonly" value="https://bitbucket.org/galaxyp/galaxyp-toolshed-peptideshaker">
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1258
1259 <dl class="metadata">
1260 <dt>Owner</dt>
1261 <dd><a href="/galaxyp">galaxyp</a></dd>
1262
1263
1264
1265 <dt>Access level</dt>
1266 <dd>Public</dd>
1267
1268 <dt>Type</dt>
1269 <dd>Mercurial</dd>
1270
1271
1272
1273 <dt>Last updated</dt>
1274 <dd><time datetime="2013-06-20T00:19:56.024767">16 hours ago</time></dd>
1275
1276 <dt>Created</dt>
1277 <dd><time datetime="2013-02-25T17:50:29.792158">2013-02-25</time></dd>
1278
1279 <dt>Size</dt>
1280 <dd>
1281 1.4 MB
1282 <a rel="nofollow"
1283
1284 href="/galaxyp/galaxyp-toolshed-peptideshaker/get/80ef7cf0d97a.zip"
1285
1286 >(download)</a>
1287 </dd>
1288
1289
1290
1291 </dl>
1292 </section>
1293
1294
1295
1296
1297
1298 </div>
1299 <div class="clearfix"></div>
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