Mercurial > repos > pjbriggs > macs21

changeset 23:c7646ff9b5c9 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload commit a2f39c10087e77bde5b5db5d04305f72b8eb2af2
author pjbriggs
date Tue, 27 Jun 2023 07:37:07 +0000
parents dfb939015935
children
files README.rst install_tool_deps.sh macs21_wrapper.xml package_macs21_wrapper.sh run_planemo_tests.sh test-data/test_MACS2.1.1_peaks.xls.re_match~
diffstat 6 files changed, 93 insertions(+), 50 deletions(-) [+]
line wrap: on
line diff
--- a/README.rst	Wed Dec 12 07:55:16 2018 -0500
+++ b/README.rst	Tue Jun 27 07:37:07 2023 +0000
@@ -56,21 +56,22 @@
 to re-implement the internal workings of the tool to conform with current
 practices in invoking commands from Galaxy, and to add new functionality.
 
-========== ======================================================================
-Version    Changes
----------- ----------------------------------------------------------------------
-2.1.2.0    - Update to use MACS 2.1.2
-2.1.1.0    - Update to use MACS 2.1.1 and use conda to resolve dependencies
-2.1.0-6    - Add bedSort step into bigWig file generation; terminate with error
-             when MACS finishes with non-zero exit code.
-2.1.0-5    - User must explicitly specify the format for the inputs (to allow
-             for paired-end data)
-2.1.0-4    - Remove 'bdgcmp' functionality.
-2.1.0-3    - Add tool tests
-2.1.0-2    - Add option to create bigWig file from bedGraphs; fix bug with -B
-             option; make --mfold defaults consistent.
-2.1.0-1    - Initial version
-========== ======================================================================
+============= =================================================================
+Version       Changes
+------------- -----------------------------------------------------------------
+2.1.2-galaxy1 - Update UCSC tool dependencies to version 357
+2.1.2.0       - Update to use MACS 2.1.2
+2.1.1.0       - Update to use MACS 2.1.1 and use conda to resolve dependencies
+2.1.0-6       - Add bedSort step into bigWig file generation; terminate with
+                error when MACS finishes with non-zero exit code.
+2.1.0-5       - User must explicitly specify the format for the inputs (to
+                allow for paired-end data)
+2.1.0-4       - Remove 'bdgcmp' functionality.
+2.1.0-3       - Add tool tests
+2.1.0-2       - Add option to create bigWig file from bedGraphs; fix bug with
+                ``-B`` option; make ``--mfold`` defaults consistent.
+2.1.0-1       - Initial version
+============= =================================================================
 
 
 Developers
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/install_tool_deps.sh	Tue Jun 27 07:37:07 2023 +0000
@@ -0,0 +1,30 @@
+#!/bin/bash
+#
+# Install the tool dependencies for MACS21 for testing from command line
+#
+# Installer functions
+. $(dirname $0)/../../local_dependency_installers/numpy.sh
+. $(dirname $0)/../../local_dependency_installers/macs2.sh
+. $(dirname $0)/../../local_dependency_installers/ucsc_tools.sh
+#
+# Installation directory
+TOP_DIR=$1
+if [ -z "$TOP_DIR" ] ; then
+    echo Usage: $(basename $0) DIR
+    exit
+fi
+if [ -z "$(echo $TOP_DIR | grep ^/)" ] ; then
+    TOP_DIR=$(pwd)/$TOP_DIR
+fi
+if [ ! -d "$TOP_DIR" ] ; then
+    mkdir -p $TOP_DIR
+fi
+# Numpy 1.9
+install_numpy_1_9 $TOP_DIR
+# MACS21
+. $TOP_DIR/numpy/1.9/env.sh # needs Numpy 1.9
+install_macs2_2_1_0_20140616 $TOP_DIR
+# UCSC tool subset
+install_ucsc_tools_for_macs21_2_0 $TOP_DIR
+##
+#
--- a/macs21_wrapper.xml	Wed Dec 12 07:55:16 2018 -0500
+++ b/macs21_wrapper.xml	Tue Jun 27 07:37:07 2023 +0000
@@ -1,13 +1,13 @@
-<tool id="macs2_1_peakcalling" name="MACS2.1.2" version="2.1.2.0">
+<tool id="macs2_1_peakcalling" name="MACS2.1.2" version="2.1.2-galaxy1">
   <description>Model-based Analysis of ChIP-Seq: peak calling</description>
   <requirements>
     <requirement type="package" version="2.7">python</requirement>
     <requirement type="package" version="2.1.2">macs2</requirement>
     <requirement type="package" version="3.5">R</requirement>
-    <requirement type="package" version="357">ucsc-fetchchromsizes</requirement>
-    <requirement type="package" version="357">ucsc-bedclip</requirement>
-    <requirement type="package" version="357">ucsc-bedsort</requirement>
-    <requirement type="package" version="357">ucsc-bedgraphtobigwig</requirement>
+    <requirement type="package" version="377">ucsc-fetchchromsizes</requirement>
+    <requirement type="package" version="377">ucsc-bedclip</requirement>
+    <requirement type="package" version="377">ucsc-bedsort</requirement>
+    <requirement type="package" version="377">ucsc-bedgraphtobigwig</requirement>
   </requirements>
   <version_command>macs2 --version</version_command>
   <command><![CDATA[
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/package_macs21_wrapper.sh	Tue Jun 27 07:37:07 2023 +0000
@@ -0,0 +1,24 @@
+#!/bin/sh
+#
+# Package MACS 2.1 files into tgz file for upload to
+# Galaxy toolshed
+#
+VERSION=$(grep "^<tool" macs21_wrapper.xml | grep -o -e version=\".*\" | cut -d= -f2 | tr -d \")
+TGZ=macs21-${VERSION}.tgz
+if [ -f $TGZ ] ; then
+    echo $TGZ: already exists, please remove >&2
+    exit 1
+fi
+tar cvzf $TGZ \
+    README.rst \
+    macs21_wrapper.xml \
+    macs21_wrapper.py \
+    test-data
+if [ -f $TGZ ] ; then
+    echo Created $TGZ
+else
+    echo Failed to created $TGZ >&2
+    exit 1
+fi
+##
+#
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/run_planemo_tests.sh	Tue Jun 27 07:37:07 2023 +0000
@@ -0,0 +1,18 @@
+#!/bin/bash
+#
+# Install dependencies and set up environment for
+# the macs21 tool, then run tests using planemo
+#
+# Note that any arguments supplied to the script are
+# passed directly to the "planemo test..." invocation
+#
+# e.g. --install_galaxy (to get planemo to create a
+#                        Galaxy instance to run tests)
+#
+#      --galaxy_root DIR (to run tests using existing
+#                         Galaxy instance)
+#
+# Run the planemo tests
+planemo test $@ $(dirname $0)/macs21_wrapper.xml
+##
+#
--- a/test-data/test_MACS2.1.1_peaks.xls.re_match~	Wed Dec 12 07:55:16 2018 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,30 +0,0 @@
-\#peaks\ file
-\#\ This\ file\ is\ generated\ by\ MACS\ version\ 2\.1\.1\.20160309
-\#\ Command\ line\:\ callpeak\ \-t\ \/tmp\/tmpHxmla3\/files\/000\/dataset\_9\.dat\ \-c\ \/tmp\/tmpHxmla3\/files\/000\/dataset\_10\.dat\ \-\-format\=BED\ \-\-name\=test\_MACS2\.1\.1\ \-\-bw\=300\ \-\-gsize\=775000000\.0\ \-\-nomodel\ \-\-extsize\=243\ \-\-qvalue\=0\.05\ \-B\ \-\-SPMR\ \-\-mfold\ 5\ 50\ \-\-keep\-dup\ 1
-\#\ ARGUMENTS\ LIST\:
-\#\ name\ \=\ test\_MACS2\.1\.1
-\#\ format\ \=\ BED
-\#\ ChIP\-seq\ file\ \=\ \[\'\/tmp\/tmpHxmla3\/files\/000\/dataset\_9\.dat\'\]
-\#\ control\ file\ \=\ \[\'\/tmp\/tmpHxmla3\/files\/000\/dataset\_10\.dat\'\]
-\#\ effective\ genome\ size\ \=\ 7\.75e\+08
-\#\ band\ width\ \=\ 300
-\#\ model\ fold\ \=\ \[5\,\ 50\]
-\#\ qvalue\ cutoff\ \=\ 5\.00e\-02
-\#\ Larger\ dataset\ will\ be\ scaled\ towards\ smaller\ dataset\.
-\#\ Range\ for\ calculating\ regional\ lambda\ is\:\ 1000\ bps\ and\ 10000\ bps
-\#\ Broad\ region\ calling\ is\ off
-\#\ Paired\-End\ mode\ is\ off
-\#\ MACS\ will\ save\ fragment\ pileup\ signal\ per\ million\ reads
-
-\#\ tag\ size\ is\ determined\ as\ 50\ bps
-\#\ total\ tags\ in\ treatment\:\ 50
-\#\ tags\ after\ filtering\ in\ treatment\:\ 50
-\#\ maximum\ duplicate\ tags\ at\ the\ same\ position\ in\ treatment\ \=\ 1
-\#\ Redundant\ rate\ in\ treatment\:\ 0\.00
-\#\ total\ tags\ in\ control\:\ 50
-\#\ tags\ after\ filtering\ in\ control\:\ 50
-\#\ maximum\ duplicate\ tags\ at\ the\ same\ position\ in\ control\ \=\ 1
-\#\ Redundant\ rate\ in\ control\:\ 0\.00
-\#\ d\ \=\ 243
-\#chr\	start\	end\	length\	abs\_summit\	pileup\	\-log10\(pvalue\)\	fold\_enrichment\	\-log10\(qvalue\)\	name
-chr26\	4118914\	4119282\	369\	4119130\	9\.00\	9\.13132\	6\.31632\	2\.51561\	test\_MACS2\.1\.1\_peak\_1