Mercurial > repos > peterjc > seq_composition
comparison tools/seq_composition/README.rst @ 2:4283011f4be2 draft
v0.0.3 Internal Python style updates
| author | peterjc |
|---|---|
| date | Wed, 01 Feb 2017 10:00:22 -0500 |
| parents | c0eb0e5792f3 |
| children | 7a26bb458806 |
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| 1:c0eb0e5792f3 | 2:4283011f4be2 |
|---|---|
| 1 Galaxy tool reporting sequence composition | 1 Galaxy tool reporting sequence composition |
| 2 ========================================== | 2 ========================================== |
| 3 | 3 |
| 4 This tool is copyright 2014-2015 by Peter Cock, The James Hutton Institute | 4 This tool is copyright 2014-2017 by Peter Cock, The James Hutton Institute |
| 5 (formerly SCRI, Scottish Crop Research Institute), UK. All rights reserved. | 5 (formerly SCRI, Scottish Crop Research Institute), UK. All rights reserved. |
| 6 See the licence text below (MIT licence). | 6 See the licence text below (MIT licence). |
| 7 | 7 |
| 8 This tool is a short Python script (using Biopython library functions) to | 8 This tool is a short Python script (using Biopython library functions) to |
| 9 loop over given sequence files (in a range of formats including FASTA, FASTQ, | 9 loop over given sequence files (in a range of formats including FASTA, FASTQ, |
| 58 ------- ---------------------------------------------------------------------- | 58 ------- ---------------------------------------------------------------------- |
| 59 v0.0.1 - Initial version. | 59 v0.0.1 - Initial version. |
| 60 - Tool definition now embeds citation information. | 60 - Tool definition now embeds citation information. |
| 61 v0.0.2 - Reorder XML elements (internal change only). | 61 v0.0.2 - Reorder XML elements (internal change only). |
| 62 - Planemo for Tool Shed upload (``.shed.yml``, internal change only). | 62 - Planemo for Tool Shed upload (``.shed.yml``, internal change only). |
| 63 v0.0.3 - Python style updates (internal change only). | |
| 63 ======= ====================================================================== | 64 ======= ====================================================================== |
| 64 | 65 |
| 65 | 66 |
| 66 Developers | 67 Developers |
| 67 ========== | 68 ========== |
| 72 | 73 |
| 73 For pushing a release to the test or main "Galaxy Tool Shed", use the following | 74 For pushing a release to the test or main "Galaxy Tool Shed", use the following |
| 74 Planemo commands (which requires you have set your Tool Shed access details in | 75 Planemo commands (which requires you have set your Tool Shed access details in |
| 75 ``~/.planemo.yml`` and that you have access rights on the Tool Shed):: | 76 ``~/.planemo.yml`` and that you have access rights on the Tool Shed):: |
| 76 | 77 |
| 77 $ planemo shed_upload --shed_target testtoolshed --check_diff ~/repositories/pico_galaxy/tools/seq_composition/ | 78 $ planemo shed_update -t testtoolshed --check_diff ~/repositories/pico_galaxy/tools/seq_composition/ |
| 78 ... | 79 ... |
| 79 | 80 |
| 80 or:: | 81 or:: |
| 81 | 82 |
| 82 $ planemo shed_upload --shed_target toolshed --check_diff ~/repositories/pico_galaxy/tools/seq_composition/ | 83 $ planemo shed_update -t toolshed --check_diff ~/repositories/pico_galaxy/tools/seq_composition/ |
| 83 ... | 84 ... |
| 84 | 85 |
| 85 To just build and check the tar ball, use:: | 86 To just build and check the tar ball, use:: |
| 86 | 87 |
| 87 $ planemo shed_upload --tar_only ~/repositories/pico_galaxy/tools/seq_composition/ | 88 $ planemo shed_upload --tar_only ~/repositories/pico_galaxy/tools/seq_composition/ |