Merge pull request #163 from drpatelh/master

Update environment

Author: drpatelh

CHANGELOG.md

@@ -52,23 +52,23 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.
 * Update gawk `4.2.1` -> `5.1.0`
 * Update r-base `3.4.1` -> `3.6.2`
 * Update r-optparse `1.6.0` -> `1.6.6`
-* Update r-ggplot2 `3.1.0` -> `3.3.0`
+* Update r-ggplot2 `3.1.0` -> `3.3.2`
 * Update r-pheatmap `1.0.10` -> `1.0.12`
 * Update r-lattice `0.20_35` -> `0.20_41`
 * Update r-upsetr `1.3.3` -> `1.4.0`
 * Update r-scales `1.0.0` -> `1.1.1`
-* Update r-xfun `0.3` -> `0.14`
+* Update r-xfun `0.3` -> `0.15`
 * Update fastqc `0.11.8` -> `0.11.9`
 * Update trim-galore `0.5.0` -> `0.6.5`
 * Update samtools `1.9` -> `1.10`
-* Update picard `2.19.0` -> `2.22.8`
+* Update picard `2.19.0` -> `2.23.1`
 * Update pysam `0.15.2` -> `0.15.3`
 * Update bedtools `2.27.1` -> `2.29.2`
 * Update ucsc-bedgraphtobigwig `377` -> `357`
 * Update deeptools `3.2.1` -> `3.4.3`
 * Update macs2 `2.1.2` -> `2.2.7.1`
 * Update homer `4.9.1` -> `4.11`
-* Update subread `1.6.4` -> `2.0.0`
+* Update subread `1.6.4` -> `2.0.1`
 * Update multiqc `1.7` -> `1.8`  
 * Update phantompeakqualtools `1.2` -> `1.2.2`
 * Update bioconductor-deseq2 `1.20.0` -> `1.26.0`

bin/scrape_software_versions.py

@@ -13,7 +13,7 @@
     'BEDTools': ['v_bedtools.txt', r"bedtools v(\S+)"],
     'BamTools': ['v_bamtools.txt', r"bamtools (\S+)"],
     'deepTools': ['v_deeptools.txt', r"plotFingerprint (\S+)"],
-    'Picard': ['v_picard.txt', r"([\d\.]+)-SNAPSHOT"],
+    'Picard': ['v_picard.txt', r"\n(\S+)"],
     'R': ['v_R.txt', r"R version (\S+)"],
     'Pysam': ['v_pysam.txt', r"(\S+)"],
     'MACS2': ['v_macs2.txt', r"macs2 (\S+)"],

environment.yml

@@ -15,13 +15,13 @@ dependencies:
   - conda-forge::r-optparse=1.6.6
   - conda-forge::r-rcolorbrewer=1.1_2
   - conda-forge::r-reshape2=1.4.4
-  - conda-forge::r-ggplot2=3.3.0
+  - conda-forge::r-ggplot2=3.3.2
   - conda-forge::r-tidyr=1.1.0
   - conda-forge::r-scales=1.1.1
   - conda-forge::r-pheatmap=1.0.12
   - conda-forge::r-lattice=0.20_41
   - conda-forge::r-upsetr=1.4.0
-  - conda-forge::r-xfun=0.14
+  - conda-forge::r-xfun=0.15
   - conda-forge::gawk=5.1.0
   - conda-forge::pigz=2.3.4               ## Required for TrimGalore multi-threading
 
@@ -30,15 +30,15 @@ dependencies:
   - bioconda::trim-galore=0.6.5
   - bioconda::bwa=0.7.17
   - bioconda::samtools=1.10
-  - bioconda::picard=2.22.8
+  - bioconda::picard=2.23.1
   - bioconda::bamtools=2.5.1
   - bioconda::pysam=0.15.3
   - bioconda::bedtools=2.29.2
   - bioconda::ucsc-bedgraphtobigwig=357
   - bioconda::deeptools=3.4.3
   - bioconda::macs2=2.2.7.1
   - bioconda::homer=4.11
-  - bioconda::subread=2.0.0
+  - bioconda::subread=2.0.1
   - bioconda::phantompeakqualtools=1.2.2
   - bioconda::preseq=2.0.3
   - bioconda::multiqc=1.9