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Updated to version 0.02.04.4 (new pal_filter script)
author pjbriggs
date Wed, 24 Feb 2016 08:25:17 -0500
parents b6ccc7dd7b02
children a73c48890bde
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2:b6ccc7dd7b02 3:e1a14ed7a9d6
19 - ``pal_finder_wrapper.sh`` (the shell script wrapper) 19 - ``pal_finder_wrapper.sh`` (the shell script wrapper)
20 - ``pal_finder_filter_and_assembly.py`` (filtering utility) 20 - ``pal_finder_filter_and_assembly.py`` (filtering utility)
21 21
22 The suggested location is in a ``tools/pal_finder_wrapper/`` folder. You will then 22 The suggested location is in a ``tools/pal_finder_wrapper/`` folder. You will then
23 need to modify the ``tools_conf.xml`` file to tell Galaxy to offer the tool 23 need to modify the ``tools_conf.xml`` file to tell Galaxy to offer the tool
24 by adding the line: 24 by adding the line::
25 25
26 <tool file="pal_finder/pal_finder_wrapper.xml" /> 26 <tool file="pal_finder/pal_finder_wrapper.xml" />
27 27
28 You will also need to install the pal_finder and primer3 packages: 28 You will also need to install the pal_finder and primer3 packages:
29 29
46 and simple.ref; defaults to /usr/share/pal_finder_v0.02.04) 46 and simple.ref; defaults to /usr/share/pal_finder_v0.02.04)
47 - ``PRIMER3_CORE_EXE``: name of the primer3_core program, which should include the 47 - ``PRIMER3_CORE_EXE``: name of the primer3_core program, which should include the
48 full path if it's not on the Galaxy user's PATH (defaults to primer3_core) 48 full path if it's not on the Galaxy user's PATH (defaults to primer3_core)
49 49
50 If you want to run the functional tests, copy the sample test files under 50 If you want to run the functional tests, copy the sample test files under
51 sample test files under Galaxy's ``test-data/`` directory. Then: 51 sample test files under Galaxy's ``test-data/`` directory. Then::
52 52
53 ./run_tests.sh -id microsat_pal_finder 53 ./run_tests.sh -id microsat_pal_finder
54 54
55 You will need to have set the environment variables above. 55 You will need to have set the environment variables above.
56 56
58 ======= 58 =======
59 59
60 ========== ====================================================================== 60 ========== ======================================================================
61 Version Changes 61 Version Changes
62 ---------- ---------------------------------------------------------------------- 62 ---------- ----------------------------------------------------------------------
63 0.02.04.4 - Update to the filter script (``pal_filter.py``) which removes some
64 columns from the output assembly file.
63 0.02.04.3 - Update to the Illumina filtering script from Graeme Fox (including 65 0.02.04.3 - Update to the Illumina filtering script from Graeme Fox (including
64 new option to run ``PANDASeq`` assembly/QC steps), and corresponding 66 new option to run ``PANDASeq`` assembly/QC steps), and corresponding
65 update to the tool; add support for input FASTQs to be a dataset 67 update to the tool; add support for input FASTQs to be a dataset
66 collection pair. 68 collection pair.
67 0.02.04.2 - Fix bug that causes tool to fail when prefix includes spaces; 69 0.02.04.2 - Fix bug that causes tool to fail when prefix includes spaces;