Mercurial > repos > peterjc > mira_assembler

comparison tools/mira3/README.rst @ 25:56dede4f0735 draft

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planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira3/ commit 9526de68e38a82bb84b2d9267a8c290c6adcaa65
author peterjc
date Fri, 15 Sep 2017 10:08:39 -0400
parents 83a94a5038a7
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24:ad14a345f1b0 25:56dede4f0735
8 This tool is a short Python script (to collect the MIRA output and move it 8 This tool is a short Python script (to collect the MIRA output and move it
9 to where Galaxy expects the files, and convert MIRA's TCS file into a tab 9 to where Galaxy expects the files, and convert MIRA's TCS file into a tab
10 separated file for use in Galaxy). 10 separated file for use in Galaxy).
11 11
12 It is available from the Galaxy Tool Shed at: 12 It is available from the Galaxy Tool Shed at:
13 http://toolshed.g2.bx.psu.edu/view/peterjc/mira_assembler 13 http://toolshed.g2.bx.psu.edu/view/peterjc/mira_assembler
14 14
15 15
16 Automated Installation 16 Automated Installation
17 ====================== 17 ======================
18 18
30 * ``mira.xml`` (the Galaxy tool definition) 30 * ``mira.xml`` (the Galaxy tool definition)
31 31
32 The suggested location is a new ``tools/mira3`` folder. You will also need to 32 The suggested location is a new ``tools/mira3`` folder. You will also need to
33 modify the ``tools_conf.xml`` file to tell Galaxy to offer the tool by adding 33 modify the ``tools_conf.xml`` file to tell Galaxy to offer the tool by adding
34 the line:: 34 the line::
35 35
36 <tool file="mira3/mira.xml" /> 36 <tool file="mira3/mira.xml" />
37 37
38 If you wish to run the unit tests, also move/copy the ``test-data/`` files 38 If you wish to run the unit tests, also move/copy the ``test-data/`` files
39 under Galaxy's ``test-data/`` folder. Then:: 39 under Galaxy's ``test-data/`` folder. Then::
40 40
114 114
115 To just build and check the tar ball, use:: 115 To just build and check the tar ball, use::
116 116
117 $ planemo shed_upload --tar_only tools/mira3/ 117 $ planemo shed_upload --tar_only tools/mira3/
118 ... 118 ...
119 $ tar -tzf shed_upload.tar.gz 119 $ tar -tzf shed_upload.tar.gz
120 test-data/empty_file.dat 120 test-data/empty_file.dat
121 test-data/tvc_contigs.fasta 121 test-data/tvc_contigs.fasta
122 test-data/tvc_mini.fastq 122 test-data/tvc_mini.fastq
123 tools/mira3/README.rst 123 tools/mira3/README.rst
124 tools/mira3/mira.py 124 tools/mira3/mira.py