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dpryan79dpryan79
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Merge branch 'release/3.0.1'
2 parents 7d156a7 + fa58d09 commit 72ae8f6

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-37
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9 files changed

+59
-37
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‎.planemo.sh‎

Lines changed: 25 additions & 20 deletions
Original file line numberDiff line numberDiff line change
@@ -1,24 +1,29 @@
11
#!/bin/bash
22
planemo=$HOME/miniconda/envs/planemo/bin/planemo
33

4-
$planemo test --no_dependency_resolution --install_galaxy \
5-
galaxy/wrapper/alignmentSieve.xml \
6-
galaxy/wrapper/bamCompare.xml \
7-
galaxy/wrapper/bamCoverage.xml \
8-
galaxy/wrapper/bamPEFragmentSize.xml \
9-
galaxy/wrapper/bigwigCompare.xml \
10-
galaxy/wrapper/computeGCBias.xml \
11-
galaxy/wrapper/computeMatrix.xml \
12-
galaxy/wrapper/computeMatrixOperations.xml \
13-
galaxy/wrapper/correctGCBias.xml \
14-
galaxy/wrapper/estimateReadFiltering.xml \
15-
galaxy/wrapper/multiBamSummary.xml \
16-
galaxy/wrapper/multiBigwigSummary.xml \
17-
galaxy/wrapper/plotCorrelation.xml \
18-
galaxy/wrapper/plotCoverage.xml \
19-
galaxy/wrapper/plotEnrichment.xml \
20-
galaxy/wrapper/plotFingerprint.xml \
21-
galaxy/wrapper/plotHeatmap.xml \
22-
galaxy/wrapper/plotPCA.xml \
23-
galaxy/wrapper/plotProfiler.xml 2>&1 | grep -v -e "^galaxy" | grep -v -e "^requests"
4+
if [[ $1 == "1" ]] ; then
5+
wrappers="galaxy/wrapper/alignmentSieve.xml \
6+
galaxy/wrapper/bamCompare.xml \
7+
galaxy/wrapper/bamCoverage.xml \
8+
galaxy/wrapper/bamPEFragmentSize.xml \
9+
galaxy/wrapper/bigwigCompare.xml \
10+
galaxy/wrapper/computeGCBias.xml"
11+
elif [[ $1 == "2" ]] ; then
12+
wrappers="galaxy/wrapper/computeMatrix.xml \
13+
galaxy/wrapper/computeMatrixOperations.xml \
14+
galaxy/wrapper/correctGCBias.xml \
15+
galaxy/wrapper/estimateReadFiltering.xml \
16+
galaxy/wrapper/multiBamSummary.xml \
17+
galaxy/wrapper/multiBigwigSummary.xml"
18+
else
19+
wrappers="galaxy/wrapper/plotCorrelation.xml \
20+
galaxy/wrapper/plotCoverage.xml \
21+
galaxy/wrapper/plotEnrichment.xml \
22+
galaxy/wrapper/plotFingerprint.xml \
23+
galaxy/wrapper/plotHeatmap.xml \
24+
galaxy/wrapper/plotPCA.xml \
25+
galaxy/wrapper/plotProfiler.xml"
26+
fi
27+
28+
${planemo} test --no_dependency_resolution --install_galaxy ${wrappers} 2>&1 | grep -v -e "^galaxy" | grep -v -e "^requests"
2429
test ${PIPESTATUS[0]} -eq 0

‎.travis.yml‎

Lines changed: 17 additions & 8 deletions
Original file line numberDiff line numberDiff line change
@@ -7,10 +7,18 @@ os:
77
- osx
88
jobs:
99
include:
10-
- stage: galaxy36
10+
- stage: galaxy36_1
1111
env:
1212
- TESTGALAXY="1"
1313
- TRAVIS_PYTHON_VERSION=3.6
14+
- stage: galaxy36_2
15+
env:
16+
- TESTGALAXY="2"
17+
- TRAVIS_PYTHON_VERSION=3.6
18+
- stage: galaxy36_3
19+
env:
20+
- TESTGALAXY="3"
21+
- TRAVIS_PYTHON_VERSION=3.6
1422

1523
# Setup anaconda
1624
before_install:
@@ -23,7 +31,7 @@ before_install:
2331
- hash -r
2432
- conda config --set always_yes yes --set changeps1 no
2533
- conda update -q conda
26-
- if [[ "$TRAVIS_OS_NAME" == "linux" && "$TRAVIS_PYTHON_VERSION" == "3.6" && ${TESTGALAXY:-"0"} == "1" ]] ; then conda create -c conda-forge -c bioconda -n planemo planemo; fi
34+
- if [[ "$TRAVIS_OS_NAME" == "linux" && "$TRAVIS_PYTHON_VERSION" == "3.6" && ${TESTGALAXY:-"0"} != "0" ]] ; then conda create -c conda-forge -c bioconda -n planemo planemo; fi
2735

2836
# Useful for debugging any issues with conda
2937
- conda info -a
@@ -35,11 +43,12 @@ install:
3543

3644
# command to run tests
3745
script:
38-
- if [[ ${TESTGALAXY:-"2"} == "2" ]] ; then flake8 . --exclude=.venv,.build,foo,build,deeptoolsintervals/__init__.py --ignore=E501,F403,E402,F999,F405,E722 ; fi
39-
- if [[ ${TESTGALAXY:-"2"} == "2" ]] ; then export owd=`pwd` ; fi
40-
- if [[ ${TESTGALAXY:-"2"} == "2" ]] ; then cd ~/ && nosetests --with-doctest -sv deeptools ; fi
41-
- if [[ ${TESTGALAXY:-"2"} == "2" ]] ; then nosetests --with-doctest -sv deeptoolsintervals ; fi
42-
- if [[ ${TESTGALAXY:-"2"} == "2" ]] ; then cd ${owd} ; fi
46+
- if [[ ${TESTGALAXY:-"0"} == "0" ]] ; then flake8 . --exclude=.venv,.build,foo,build,deeptoolsintervals/__init__.py --ignore=E501,F403,E402,F999,F405,E722 ; fi
47+
- if [[ ${TESTGALAXY:-"0"} == "0" ]] ; then export owd=`pwd` ; fi
48+
- if [[ ${TESTGALAXY:-"0"} == "0" ]] ; then cd ~/ && nosetests --with-doctest -sv deeptools ; fi
49+
- if [[ ${TESTGALAXY:-"0"} == "0" ]] ; then nosetests --with-doctest -sv deeptoolsintervals ; fi
50+
- if [[ ${TESTGALAXY:-"0"} == "0" ]] ; then cd ${owd} ; fi
4351
- if [[ "$TRAVIS_OS_NAME" == "linux" && ${TESTGALAXY:-"0"} == "1" ]] ; then /home/travis/miniconda/envs/planemo/bin/planemo lint galaxy/wrapper/ ; fi
44-
- if [[ "$TRAVIS_OS_NAME" == "linux" && ${TESTGALAXY:-"0"} == "1" ]] ; then ./.planemo.sh ; fi
52+
- if [[ "$TRAVIS_OS_NAME" == "linux" && ${TESTGALAXY:-"0"} != "0" ]] ; then ./.planemo.sh ${TESTGALAXY}; fi
53+
4554
sudo: false

‎CHANGES.txt‎

Lines changed: 5 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -1,3 +1,8 @@
1+
3.0.1
2+
3+
* Fixed the `--perGroup` option in plotProfile and plotHeatmap when multiple groups were being used. In version 3.0.0, this would typically cause an error and deepTools to crash. (issue #673)
4+
* Fixed a few issues with the Galaxy wrappers. Thanks to Ralf Gilsbach, Claudia Keller, and @bgruening (e.g., issue #678)
5+
16
3.0.0
27

38
* plotCorrelation` now has `--log1p` and `--maxRange` options if a scatter plot is produced. `--log1p` plots the natural log of the values (plus 1). `--maxRange` sets the maximum X and Y axis ranges. If they would normally be below this value then they are left unchanged. (issue #536)

‎deeptools/_version.py‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -2,4 +2,4 @@
22
# This file is originally generated from Git information by running 'setup.py
33
# version'. Distribution tarballs contain a pre-generated copy of this file.
44

5-
__version__ = '3.0.0'
5+
__version__ = '3.0.1'

‎deeptools/plotHeatmap.py‎

Lines changed: 3 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -128,8 +128,10 @@ def addProfilePlot(hm, plt, fig, grids, iterNum, iterNum2, perGroup, averageType
128128
for sample_id in range(iterNum):
129129
if perGroup:
130130
title = hm.matrix.group_labels[sample_id]
131+
tickIdx = sample_id % hm.matrix.get_num_samples()
131132
else:
132133
title = hm.matrix.sample_labels[sample_id]
134+
tickIdx = sample_id
133135
if sample_id > 0 and len(yMin) == 1 and len(yMax) == 1:
134136
ax_profile = fig.add_subplot(grids[0, sample_id], sharey=ax_list[0])
135137
else:
@@ -157,7 +159,7 @@ def addProfilePlot(hm, plt, fig, grids, iterNum, iterNum2, perGroup, averageType
157159

158160
if sample_id == 0 and yAxisLabel != '':
159161
ax_profile.set_ylabel(yAxisLabel)
160-
xticks, xtickslabel = hm.getTicks(sample_id)
162+
xticks, xtickslabel = hm.getTicks(tickIdx)
161163
if np.ceil(max(xticks)) != float(sub_matrix['matrix'].shape[1]):
162164
tickscale = float(sub_matrix['matrix'].shape[1]) / max(xticks)
163165
xticks_use = [x * tickscale for x in xticks]

‎deeptools/plotProfile.py‎

Lines changed: 3 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -698,10 +698,12 @@ def plot_profile(self):
698698
title = self.hm.matrix.group_labels[plot]
699699
if row != 0 and len(self.y_min) == 1 and len(self.y_max) == 1:
700700
plt.setp(ax.get_yticklabels(), visible=False)
701+
tickIdx = plot % self.hm.matrix.get_num_samples()
701702
else:
702703
title = self.hm.matrix.sample_labels[plot]
703704
if col != 0 and len(self.y_min) == 1 and len(self.y_max) == 1:
704705
plt.setp(ax.get_yticklabels(), visible=False)
706+
tickIdx = plot
705707

706708
ax.set_title(title)
707709
for data_idx in range(self.numlines):
@@ -747,7 +749,7 @@ def plot_profile(self):
747749
"""
748750

749751
totalWidth = sub_matrix['matrix'].shape[1]
750-
xticks, xtickslabel = self.getTicks(plot)
752+
xticks, xtickslabel = self.getTicks(tickIdx)
751753
if np.ceil(max(xticks)) != float(totalWidth):
752754
tickscale = float(totalWidth) / max(xticks)
753755
xticks_use = [x * tickscale for x in xticks]

‎galaxy/wrapper/computeMatrix.xml‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -21,7 +21,7 @@
2121
$mode.mode_select
2222
--regionsFileName '#echo "' '".join($bed_files)#'
2323
24-
--scoreFileName '#echo "' '".join($files)#'
24+
--scoreFileName #echo ' '.join($files)#
2525
2626
--outFileName '$outFileName'
2727

‎galaxy/wrapper/deepTools_macros.xml‎

Lines changed: 2 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -1,10 +1,10 @@
11
<macros>
22

33
<token name="@THREADS@">--numberOfProcessors "\${GALAXY_SLOTS:-4}"</token>
4-
<token name="@WRAPPER_VERSION@">3.0.0</token>
4+
<token name="@WRAPPER_VERSION@">3.0.1</token>
55
<xml name="requirements">
66
<requirements>
7-
<requirement type="package" version="3.0.0">deeptools</requirement>
7+
<requirement type="package" version="3.0.1">deeptools</requirement>
88
<requirement type="package" version="1.7">samtools</requirement>
99
</requirements>
1010
<expand macro="stdio" />
@@ -456,7 +456,6 @@ is vital to you, select Yes below.">
456456
#for $counter, $f in enumerate($multibam_conditional.multibam_repeats):
457457
#set identifier = re.sub('[^\.\s\w\-]', '_', str($f.bamfiles.element_identifier))
458458
ln -s "${f.bamfiles}" "./${counter}.bam" &&
459-
ln -s "${f.bamfiles.metadata.bam_index}" "./${counter}.bam.bai" &&
460459
#if $f.bamfiles.ext == 'bam':
461460
ln -s '${f.bamfiles.metadata.bam_index}' './${counter}.bam.bai' &&
462461
#else:

‎galaxy/wrapper/multiBigwigSummary.xml‎

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -19,8 +19,8 @@
1919
2020
--outFileName $outFile
2121
22-
--bwfiles '#echo "' '".join($files)#'
23-
--labels #echo " ".join($labels)#
22+
--bwfiles #echo ' '.join($files)#
23+
--labels #echo ' '.join($labels)#
2424
2525
#if $outRawCounts:
2626
--outRawCounts '$outFileRawCounts'

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