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Updated to MACS 2.1.1 and use conda for dependency resolution.
author pjbriggs
date Tue, 20 Mar 2018 11:25:04 -0400
parents 00d73c812399
children 11cf21ee4242
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2:00d73c812399 3:4124781932db
1 MACS21: Model-based Analysis of ChIP-Seq (MACS 2.1.0) peak calling 1 MACS21: Model-based Analysis of ChIP-Seq (MACS 2.1) peak calling
2 ================================================================== 2 ================================================================
3 3
4 Galaxy tool wrapper for the peak calling function of MACS 2.1.0. MACS has been 4 Galaxy tool wrapper for the peak calling function of MACS 2.1. MACS has been
5 developed by Tao Lui 5 developed by Tao Lui
6 https://github.com/taoliu/MACS/ 6 https://github.com/taoliu/MACS/
7 7
8 The reference for MACS is: 8 The reference for MACS is:
9 9
13 13
14 Automated installation 14 Automated installation
15 ====================== 15 ======================
16 16
17 Installation via the Galaxy Tool Shed will take of installing the tool wrapper and 17 Installation via the Galaxy Tool Shed will take of installing the tool wrapper and
18 the MACS 2.1.0 program. 18 the MACS 2.1 program.
19 19
20 Manual Installation 20 Manual Installation
21 =================== 21 ===================
22 22
23 There are two files to install: 23 There are two files to install:
29 need to modify the ``tools_conf.xml`` file to tell Galaxy to offer the tool 29 need to modify the ``tools_conf.xml`` file to tell Galaxy to offer the tool
30 by adding the line: 30 by adding the line:
31 31
32 <tool file="macs21/macs21_wrapper.xml" /> 32 <tool file="macs21/macs21_wrapper.xml" />
33 33
34 You will also need to install MACS 2.1.0 and its dependencies: 34 You will also need to install MACS 2.1 and its dependencies:
35 35
36 - https://pypi.python.org/pypi/MACS2 36 - https://pypi.python.org/pypi/MACS2
37 37
38 and ensure that it's on your Galaxy user's ``PATH`` when running the tool. 38 and ensure that it's on your Galaxy user's ``PATH`` when running the tool.
39 39
50 by Ziru Zhou (ziruzhou@gmail.com), specifically the ``16:14f378e35191`` 50 by Ziru Zhou (ziruzhou@gmail.com), specifically the ``16:14f378e35191``
51 revision of the tool available via 51 revision of the tool available via
52 52
53 - http://toolshed.g2.bx.psu.edu/view/modencode-dcc/macs2 53 - http://toolshed.g2.bx.psu.edu/view/modencode-dcc/macs2
54 54
55 This version has been substantially modified both to adapt it to MACS 2.1.0, and 55 This version has been substantially modified both to adapt it to MACS 2.1, and
56 to re-implement the internal workings of the tool to conform with current 56 to re-implement the internal workings of the tool to conform with current
57 practices in invoking commands from Galaxy, and to add new functionality. 57 practices in invoking commands from Galaxy, and to add new functionality.
58 58
59 ========== ====================================================================== 59 ========== ======================================================================
60 Version Changes 60 Version Changes
61 ---------- ---------------------------------------------------------------------- 61 ---------- ----------------------------------------------------------------------
62 2.1.1.0 - Update to use MACS 2.1.1 and use conda to resolve dependencies
62 2.1.0-6 - Add bedSort step into bigWig file generation; terminate with error 63 2.1.0-6 - Add bedSort step into bigWig file generation; terminate with error
63 when MACS finishes with non-zero exit code. 64 when MACS finishes with non-zero exit code.
64 2.1.0-5 - User must explicitly specify the format for the inputs (to allow 65 2.1.0-5 - User must explicitly specify the format for the inputs (to allow
65 for paired-end data) 66 for paired-end data)
66 2.1.0-4 - Remove 'bdgcmp' functionality. 67 2.1.0-4 - Remove 'bdgcmp' functionality.