deeptools · WardDeb · Apr 5, 2023 · Nov 10, 2021 · Nov 18, 2022 · Feb 3, 2023
diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
@@ -34,7 +34,6 @@ jobs:
     - uses: "dpryan79/github-actions/@master"
     - name: Test deepTools
       run: |
-
         source activate foo
         nosetests --with-doctest -sv deeptools
   planemo_test:

diff --git a/CHANGES.txt b/CHANGES.txt
@@ -1,5 +1,16 @@
-3.6.0
-* Add bigwigAverage
+3.5.2
+* new subcommand: Bigwig average #1169
+* dendogram of plotCorrelation now matches each cell correctly
+* Fix label options
+* add pool
+* several other bugs fixed: #1159, #1185, #1172, #1181, #1183
+* Fix galaxy tests
+* upload artifact
+* allow 1 or 2 lines diff for bowtie2 program
+* change github action to get artifacts
+* fix plotPCA
+* try to fix old samtools installed
+* add forgotten channels
 
 3.5.1
 * cmp usage is updated to fit the recent mpl updates.

diff --git a/deeptools/_version.py b/deeptools/_version.py
@@ -2,4 +2,4 @@
 # This file is originally generated from Git information by running 'setup.py
 # version'. Distribution tarballs contain a pre-generated copy of this file.
 
-__version__ = '3.5.1'
+__version__ = '3.5.2'
diff --git a/deeptools/alignmentSieve.py b/deeptools/alignmentSieve.py
@@ -71,6 +71,11 @@ def parseArguments():
                          action='store_true',
                          help='Shift the produced BAM file or BEDPE regions as commonly done for ATAC-seq. This is equivalent to --shift 4 -5 5 -4.')
 
+    general.add_argument('--genomeChunkLength',
+                         type=int,
+                         default=int(1e6),
+                         help='Size of the genome (in bps) to be processed per thread. (Default: %(default)s)')
+
     output = parser.add_argument_group('Output arguments')
     output.add_argument('--BED',
                         action='store_true',
@@ -205,7 +210,7 @@ def filterWorker(arglist):
     chrom, start, end, args, chromDict = arglist
     fh = openBam(args.bam)
 
-    mode = 'wbu'
+    mode = 'wb'
     oname = getTempFileName(suffix='.bam')
     if args.filteredOutReads:
         onameFiltered = getTempFileName(suffix='.bam')
@@ -387,6 +392,7 @@ def main(args=None):
                     chrom_sizes,
                     blackListFileName=args.blackListFileName,
                     numberOfProcessors=args.numberOfProcessors,
+                    genomeChunkLength=args.genomeChunkLength,
                     verbose=args.verbose)
 
     res = sorted(res)  # The temp files are now in order for concatenation

diff --git a/docs/content/help_faq.rst b/docs/content/help_faq.rst
@@ -212,9 +212,15 @@ If your genome isn't included in our standard dataset then you'll need the follo
 1. **Effective genome size** - this is mostly needed for :doc:`bamCoverage <tools/bamCoverage>` and :doc:`bamCompare <tools/bamCompare>`, see :ref:`below <effgenomesize>` for details
 2. **Reference genome sequence in 2bit format** - this is needed for :doc:`computeGCBias <tools/computeGCBias>`, see :ref:`2bit <2bit>` for details
 
+.. _effgenomesize:
+
 -------------------------------------------------------------------------------
 
-.. _effgenomesize:
+How can I use a temp directory other than /tmp?
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+You can set your `$TMPDIR` environmental variable to a different directory.
+
+-------------------------------------------------------------------------------
 
 How do I calculate the effective genome size for an organism that's not in your list?
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

diff --git a/galaxy/wrapper/deepTools_macros.xml b/galaxy/wrapper/deepTools_macros.xml
@@ -368,7 +368,6 @@
     <xml name="pseudocount">
         <param argument="--pseudocount" type="text" value="1 1" label="Pseudocount" help="Small number to avoid dividing by zero. You can specify separate values for the pseudocount added to the numerator and denominator by providing two values separated by a space."/>
     </xml>
-
     <token name="@REFERENCES@">
 
 .. class:: infomark
@@ -483,7 +482,7 @@ is vital to you, select Yes below.">
     <token name="@multiple_input_bams@">
 <![CDATA[
         #if $custom_sample_labels_conditional.custom_labels_select == "Yes":
-            #set custom_labels=labels
+            #set custom_labels=$custom_sample_labels_conditional.labels
         #end if
         #set files=[]
         #set labels=[]
@@ -498,7 +497,7 @@ is vital to you, select Yes below.">
                     ln -s '${bamfile.metadata.cram_index}' './${counter}.bam.crai' &&
                 #end if
                 #silent $files.append("'%s.bam'" % $counter)
-                #silent $labels.append("'%s'" % identifier)
+                #silent $labels.append("'%s'" % $identifier)
             #end for
         #else:
             #for $counter, $f in enumerate($multibam_conditional.multibam_repeats):
@@ -522,7 +521,7 @@ is vital to you, select Yes below.">
     <token name="@multiple_input_bigwigs@">
 <![CDATA[
         #if $custom_sample_labels_conditional.custom_labels_select == "Yes":
-            #set custom_labels=labels
+            #set custom_labels=$custom_sample_labels_conditional.labels
         #end if
         #set files=[]
         #set labels=[]

diff --git a/requirements.txt b/requirements.txt
@@ -8,7 +8,7 @@ alabaster==0.7.12
     # via sphinx
 babel==2.10.1
     # via sphinx
-certifi==2021.10.8
+certifi==2022.12.7
     # via requests
 charset-normalizer==2.0.12
     # via requests
@@ -47,7 +47,7 @@ packaging==21.3
     # via
     #   matplotlib
     #   sphinx
-pillow==9.1.0
+pillow==9.3.0
     # via matplotlib
 plotly==5.7.0
     # via -r requirements.in