diff tools/protein_analysis/README @ 13:dc958c2a963a draft

Uploaded v0.2.2, adds missing test files

--- a/tools/protein_analysis/README	Wed Apr 03 11:12:31 2013 -0400
+++ b/tools/protein_analysis/README	Tue Apr 23 12:47:49 2013 -0400
@@ -19,6 +19,7 @@
 Contributions/revisions copyright 2011 Konrad Paszkiewicz. All rights reserved.
 See the included LICENCE file for details (an MIT style open source licence).
 
+
 Requirements
 ============
 
@@ -45,6 +46,7 @@
 Verify each of the tools is installed and working from the command line
 (when logged in as the Galaxy user if appropriate).
 
+
 Manual Installation
 ===================
 
@@ -93,17 +95,8 @@
 
    Leave out the lines for any tools you do not wish to use in Galaxy.
 
-4. Copy/move the following test files (from these archive) to Galaxy
-   subfolder test-data:
-
-four_human_proteins.fasta
-four_human_proteins_signalp3.tabular
-four_human_proteins_tmhmm2.tabular
-empty.fasta
-empty_tmhmm2.tabular
-empty_signalp3.tabular
-k12_ten_proteins.fasta
-k12_ten_proteins_psortb_p_terse.tabular
+4. Copy/move the test-data files (from this archive) to Galaxy's
+   subfolder test-data.
 
 5. Run the Galaxy functional tests for these new wrappers with:
 
@@ -145,6 +138,9 @@
 v0.1.3 - Added missing file whisson_et_al_rxlr_eer_cropped.hmm to Tool Shed
 v0.2.0 - Added PSORTb wrapper to the suite, based on earlier work
          contributed by Konrad Paszkiewicz.
+v0.2.1 - Use a script to create the Tool Shed tar-ball (removed some stray
+         files accidentally included previously via a wildcard).
+v0.2.2 - Include missing test files.
 
 
 Developers
@@ -159,33 +155,7 @@
 For making the "Galaxy Tool Shed" http://community.g2.bx.psu.edu/ tarball use
 the following command from the Galaxy root folder:
 
-tar -czf ~/tmhmm_signalp_etc.tar.gz tools/protein_analysis/LICENSE tools/protein_analysis/README tools/protein_analysis/suite_config.xml tools/protein_analysis/seq_analysis_utils.py tools/protein_analysis/signalp3.xml tools/protein_analysis/signalp3.py tools/protein_analysis/tmhmm2.xml tools/protein_analysis/tmhmm2.py tools/protein_analysis/promoter2.xml tools/protein_analysis/promoter2.py tools/protein_analysis/psortb.xml tools/protein_analysis/psortb.py tools/protein_analysis/wolf_psort.xml tools/protein_analysis/wolf_psort.py tools/protein_analysis/rxlr_motifs.xml tools/protein_analysis/rxlr_motifs.py tools/protein_analysis/whisson_et_al_rxlr_eer_cropped.hmm test-data/four_human_proteins.* test-data/empty.fasta test-data/empty_tmhmm2.tabular test-data/empty_signalp3.tabular test-data/k12_ten_proteins.fasta test-data/k12_ten_proteins_psortb_p_terse.tabular
-
-Check this worked:
+$ ./tools/protein_analysis/make_tmhmm_and_signalp.sh
 
-$ tar -tzf ~/tmhmm_signalp_etc.tar.gz
-tools/protein_analysis/LICENSE
-tools/protein_analysis/README
-tools/protein_analysis/suite_config.xml
-tools/protein_analysis/seq_analysis_utils.py
-tools/protein_analysis/signalp3.xml
-tools/protein_analysis/signalp3.py
-tools/protein_analysis/tmhmm2.xml
-tools/protein_analysis/tmhmm2.py
-tools/protein_analysis/promoter2.xml
-tools/protein_analysis/promoter2.py
-tools/protein_analysis/psortb.xml
-tools/protein_analysis/psortb.py
-tools/protein_analysis/wolf_psort.xml
-tools/protein_analysis/wolf_psort.py
-tools/protein_analysis/rxlr_motifs.xml
-tools/protein_analysis/rxrl_motifs.py
-tools/protein_analysis/whisson_et_al_rxlr_eer_cropped.hmm
-test-data/four_human_proteins.fasta
-test-data/four_human_proteins.signalp3.tabular
-test-data/four_human_proteins.tmhmm2.tabular
-test-data/empty.fasta
-test-data/empty_tmhmm2.tabular
-test-data/empty_signalp3.tabular
-test-data/k12_ten_proteins.fasta
-test-data/k12_ten_proteins_psortb_p_terse.tabular
+This simplifies ensuring a consistent set of files is bundled each time,
+including all the relevant test files.