Mercurial > repos > peterjc > seq_primer_clip
diff tools/seq_primer_clip/README.rst @ 4:9b074c1db68e draft
v0.0.14 galaxy_sequence_utils dependency etc
| author | peterjc |
|---|---|
| date | Thu, 02 Feb 2017 11:52:37 -0500 |
| parents | 708ce1e5ac94 |
| children | 530c8d6fedd8 |
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--- a/tools/seq_primer_clip/README.rst Thu Nov 21 10:47:23 2013 -0500 +++ b/tools/seq_primer_clip/README.rst Thu Feb 02 11:52:37 2017 -0500 @@ -1,7 +1,7 @@ Galaxy tool to primer clip (trim) FASTA, FASTQ or SFF reads =========================================================== -This tool is copyright 2011-2013 by Peter Cock, The James Hutton Institute +This tool is copyright 2011-2017 by Peter Cock, The James Hutton Institute (formerly SCRI, Scottish Crop Research Institute), UK. All rights reserved. See the licence text below (MIT licence). @@ -23,18 +23,19 @@ There are just two files to install: -* seq_primer_clip.py (the Python script) -* seq_primer_clip.xml (the Galaxy tool definition) +* ``seq_primer_clip.py`` (the Python script) +* ``seq_primer_clip.xml`` (the Galaxy tool definition) -The suggested location is a new tools/seq_primer_clip folder. You will also -need to modify the tools_conf.xml file to tell Galaxy to offer the tool:: +The suggested location is a new ``tools/seq_primer_clip/`` folder. You will +also need to modify the ``tools_conf.xml`` file to tell Galaxy to offer the +tool:: <tool file="seq_primer_clip/seq_primer_clip.xml" /> -If you wish to run the unit tests, also add this to tools_conf.xml.sample -and move/copy the test-data files under Galaxy's test-data folder. Then:: +If you wish to run the unit tests, also move/copy the ``test-data/`` files +under Galaxy's ``test-data/`` folder. Then:: - $ ./run_functional_tests.sh -id seq_primer_clip + $ ./run_tests.sh -id seq_primer_clip You will also need to install Biopython 1.54 or later. That's it. @@ -62,6 +63,14 @@ - Development moved to GitHub, https://github.com/peterjc/pico_galaxy - Renamed folder and adopted README.rst naming. v0.0.11 - Correct automated dependency definition. +v0.0.12 - Simplified XML to apply input format to output data. + - Tool definition now embeds citation information. +v0.0.13 - Use ``format_source=...`` tag. + - Reorder XML elements (internal change only). + - Planemo for Tool Shed upload (``.shed.yml``, internal change only). + - Fixed input file help text. +v0.0.14 - Updated to point at Biopython 1.67 (latest version in Tool Shed). + - Explicit dependency on ``galaxy_sequence_utils``. ======= ====================================================================== @@ -75,19 +84,24 @@ Development has now moved to a dedicated GitHub repository: https://github.com/peterjc/pico_galaxy -For making the "Galaxy Tool Shed" http://toolshed.g2.bx.psu.edu/ tarball use -the following command from the Galaxy root folder:: - $ tar -czf seq_primer_clip.tar.gz tools/seq_primer_clip/README.rst tools/seq_primer_clip/seq_primer_clip.* tools/seq_primer_clip/tool_dependencies.xml test-data/dop_primers.fasta test-data/MID4_GLZRM4E04_rnd30* +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):: -Check this worked:: + $ planemo shed_update -t testtoolshed --check_diff ~/repositories/pico_galaxy/tools/seq_primer_clip/ + ... - $ tar -tzf seq_primer_clip.tar.gz - tools/seq_primer_clip/README.rst - tools/seq_primer_clip/seq_primer_clip.xml - tools/seq_primer_clip/seq_primer_clip.py - tools/seq_primer_clip/tool_dependencies.xml - test-data/dop_primers.fasta +or:: + + $ planemo shed_update -t toolshed --check_diff ~/repositories/pico_galaxy/tools/seq_primer_clip/ + ... + +To just build and check the tar ball, use:: + + $ planemo shed_upload --tar_only ~/repositories/pico_galaxy/tools/seq_primer_clip/ + ... + $ tar -tzf shed_upload.tar.gz test-data/MID4_GLZRM4E04_rnd30.fasta test-data/MID4_GLZRM4E04_rnd30.fastqsanger test-data/MID4_GLZRM4E04_rnd30_fclip.fasta @@ -97,6 +111,11 @@ test-data/MID4_GLZRM4E04_rnd30_frclip.fastqsanger test-data/MID4_GLZRM4E04_rnd30_frclip.sff test-data/MID4_GLZRM4E04_rnd30.sff + test-data/dop_primers.fasta + tools/seq_primer_clip/README.rst + tools/seq_primer_clip/seq_primer_clip.py + tools/seq_primer_clip/seq_primer_clip.xml + tools/seq_primer_clip/tool_dependencies.xml Licence (MIT)