Mercurial > repos > peterjc > predictnls
diff tools/predictnls/README.rst @ 3:ae44396108f5 draft default tip
v0.0.8 internal changes
author | peterjc |
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date | Wed, 05 Aug 2015 12:25:47 -0400 |
parents | 9f2088ca5f6a |
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--- a/tools/predictnls/README.rst Fri Nov 21 07:00:43 2014 -0500 +++ b/tools/predictnls/README.rst Wed Aug 05 12:25:47 2015 -0400 @@ -1,12 +1,12 @@ Python re-implementation of predictNLS with Galaxy wrapper ========================================================== -This Galaxy tool is copyright 2011-2013 by Peter Cock, The James Hutton Institute +This Galaxy tool is copyright 2011-2015 by Peter Cock, The James Hutton Institute (formerly SCRI, Scottish Crop Research Institute), UK. All rights reserved. See the licence text below. -The tool consists of a Galaxy interface definition (predictnls.xml), and a Python -script (predictnls.py) which re-implements the command line tool predictNLS. This +The tool consists of a Galaxy interface definition (``predictnls.xml``), and a Python +script (``predictnls.py``) which re-implements the command line tool predictNLS. This should match the behaviour of predictNLS v1.0.20 (July 2011), the current latest release from the Rost Lab, see http://rostlab.org and their paper: @@ -30,12 +30,12 @@ =================== There are just four files which should be moved under the Galaxy tools folder, -e.g. in a tools/protein_analysis filter: +e.g. in a ``tools/protein_analysis`` filter: -* predictlns.xml (the Galaxy tool definition) -* predictlns.py (the Python script) -* predictlns.txt (this README file) -* My_NLS_list (the default set of NLS motifs from the Rost Lab) +* ``predictlns.xml`` (the Galaxy tool definition) +* ``predictlns.py`` (the Python script) +* ``predictlns.txt`` (this README file) +* ``My_NLS_list`` (the default set of NLS motifs from the Rost Lab) You will also need to modify the tools_conf.xml file to tell Galaxy to offer the tool. If you are using other protein analysis tools like TMHMM or SignalP, put @@ -64,6 +64,8 @@ - Updated citation information (Cock et al. 2013). - Development moved to GitHub, https://github.com/peterjc/pico_galaxy v0.0.7 - Tool definition now embeds citation information. +v0.0.8 - Reorder XML elements (internal change only). + - Planemo for Tool Shed upload (``.shed.yml``, internal change only). ======= ====================================================================== @@ -73,20 +75,29 @@ This script and related tools were initially developed on the following hg branch: http://bitbucket.org/peterjc/galaxy-central/src/tools -For making the "Galaxy Tool Shed" http://toolshed.g2.bx.psu.edu/ tarball use -the following command from the Galaxy root folder:: +For pushing a release to the test or main "Galaxy Tool Shed", use the following +Planemo commands (which requires you have set your Tool Shed access details in +``~/.planemo.yml`` and that you have access rights on the Tool Shed):: - $ tar -czf predictnls.tar.gz tools/predictnls/README.rst tools/predictnls/predictnls.xml tools/predictnls/predictnls.py tools/predictnls/My_NLS_list test-data/four_human_proteins.fasta test-data/four_human_proteins.predictnls.tabular + $ planemo shed_update --shed_target testtoolshed --check_diff ~/repositories/pico_galaxy/tools/predictnls/ + ... + +or:: -Check this worked:: + $ planemo shed_update --shed_target toolshed --check_diff ~/repositories/pico_galaxy/tools/predictnls/ + ... - $ tar -tzf predictnls.tar.gz - tools/predictnls/README.rst - tools/predictnls/predictnls.xml - tools/predictnls/predictnls.py - tools/predictnls/My_NLS_list +To just build and check the tar ball, use:: + + $ planemo shed_upload --tar_only ~/repositories/pico_galaxy/tools/predictnls/ + ... + $ tar -tzf shed_upload.tar.gz test-data/four_human_proteins.fasta test-data/four_human_proteins.predictnls.tabular + tools/predictnls/My_NLS_list + tools/predictnls/README.rst + tools/predictnls/predictnls.py + tools/predictnls/predictnls.xml Licence (GPL) @@ -99,7 +110,7 @@ the Rost Lab, which was released under the GPL v3. Therefore, as I consider this to be a derivative work, this too is released under the GPL v3. -Please note that the My_NLS_list should be an exact copy of the file of the -same name included with predictnls-1.0.7.tar.gz to predictnls-1.0.20.tar.gz +Please note that the ``My_NLS_list`` file should be an exact copy of the file of the +same name included with ``predictnls-1.0.7.tar.gz`` to ``predictnls-1.0.20.tar.gz`` inclusive (the list was extended in v1.0.7 in August 2010, see the change log included in those tar-balls), available from ftp://rostlab.org/predictnls/