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Version 0.02.04.3.
author pjbriggs
date Fri, 04 Dec 2015 07:43:30 -0500
parents 771ebe02636f
children e1a14ed7a9d6
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6 Automated installation 6 Automated installation
7 ====================== 7 ======================
8 8
9 Installation via the Galaxy Tool Shed will take of installing the tool wrapper and 9 Installation via the Galaxy Tool Shed will take of installing the tool wrapper and
10 the pal_finder and primer3_core programs, and setting the appropriate environment 10 the pal_finder and primer3_core programs (plus additional dependencies), and setting
11 variables. 11 the appropriate environment variables.
12 12
13 Manual Installation 13 Manual Installation
14 =================== 14 ===================
15 15
16 There are two files to install: 16 There are three files to install:
17 17
18 - ``pal_finder_wrapper.xml`` (the Galaxy tool definition) 18 - ``pal_finder_wrapper.xml`` (the Galaxy tool definition)
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 21
21 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
22 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
23 by adding the line: 24 by adding the line:
24 25
28 29
29 - ``pal_finder`` can be obtained from http://sourceforge.net/projects/palfinder/ 30 - ``pal_finder`` can be obtained from http://sourceforge.net/projects/palfinder/
30 - ``Primer3`` version 2.0.0-alpha (see the pal_finder installation notes) can be 31 - ``Primer3`` version 2.0.0-alpha (see the pal_finder installation notes) can be
31 obtained from http://primer3.sourceforge.net/releases.php 32 obtained from http://primer3.sourceforge.net/releases.php
32 33
33 The tool wrapper must be able to locate the pal_finder Perl script, the example 34 Additionally the filtering script needs ``BioPython`` and the ``PANDASeq`` program:
34 pal_finder config.txt and simple.ref data files, and the primer3_core program - the 35
35 locations of these are taken from the following enviroment variables which you will 36 - ``BioPython`` can be obtained from https://pypi.python.org/packages/source/b/biopython/
36 need to set manually: 37 - ``PANDASeq`` version 2.8.1 can be obtained from https://github.com/neufeld/pandaseq/
38
39 The tool wrapper must be able to locate the ``pal_finder_v0.02.04.pl`` script, the
40 example pal_finder ``config.txt`` and ``simple.ref`` data files, and the
41 ``primer3_core`` program - the locations of these are taken from the following
42 enviroment variables which you will need to set manually:
37 43
38 - ``PALFINDER_SCRIPT_DIR``: location of the pal_finder Perl script (defaults to /usr/bin) 44 - ``PALFINDER_SCRIPT_DIR``: location of the pal_finder Perl script (defaults to /usr/bin)
39 - ``PALFINDER_DATA_DIR``: location of the pal_finder data files (specifically config.txt 45 - ``PALFINDER_DATA_DIR``: location of the pal_finder data files (specifically config.txt
40 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)
41 - ``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
52 ======= 58 =======
53 59
54 ========== ====================================================================== 60 ========== ======================================================================
55 Version Changes 61 Version Changes
56 ---------- ---------------------------------------------------------------------- 62 ---------- ----------------------------------------------------------------------
63 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
65 update to the tool; add support for input FASTQs to be a dataset
66 collection pair.
57 0.02.04.2 - Fix bug that causes tool to fail when prefix includes spaces; 67 0.02.04.2 - Fix bug that causes tool to fail when prefix includes spaces;
58 add explicit dependency on Perl 5.16.3. 68 add explicit dependency on Perl 5.16.3.
59 0.02.04.1 - Add option to run Graeme Fox's ``pal_finder_filter.pl`` script to 69 0.02.04.1 - Add option to run Graeme Fox's ``pal_finder_filter.pl`` script to
60 filter and sort the pal_finder output (Illumina input data only). 70 filter and sort the pal_finder output (Illumina input data only).
61 Update version number to reflect the pal_finder version. 71 Update version number to reflect the pal_finder version.