update+release: RepeatMasker to 4.1.2-p1, release 1.3.1

Dfam-consortium · Apr 1, 2021 · 86b8750 · 86b8750
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commit 86b8750
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Showing 6 changed files with 11 additions and 6 deletions.
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -3,6 +3,10 @@ All notable changes to this project will be documented in this file.
 
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/).
 
+## 1.3.1 - 2021-04-01
+### Updated
+- RepeatMasker: `4.1.2` -> `4.1.2-p1`
+
 ## 1.3 - 2021-03-23
 ### Added
 - Installed `strace` in the container

diff --git a/Dockerfile b/Dockerfile
@@ -102,7 +102,7 @@ RUN cd /opt \
 
 # Configure RepeatMasker
 RUN cd /opt \
-    && tar -x -f src/RepeatMasker-4.1.2.tar.gz \
+    && tar -x -f src/RepeatMasker-4.1.2-p1.tar.gz \
     && chmod a+w RepeatMasker/Libraries \
     && cd RepeatMasker \
     && perl configure \
@@ -111,7 +111,7 @@ RUN cd /opt \
         -libdir=/opt/RepeatMasker/Libraries \
         -trf_prgm=/opt/trf \
         -default_search_engine=rmblast \
-    && cd .. && rm src/RepeatMasker-4.1.2.tar.gz
+    && cd .. && rm src/RepeatMasker-4.1.2-p1.tar.gz
 
 # Configure RepeatModeler
 RUN cd /opt \

diff --git a/README.md b/README.md
@@ -127,12 +127,12 @@ $ singularity build dfam-tetools.sif dfam-tetools.def
 
 ## Included software
 
-The following software is included in the Dfam TE Tools container (version `1.3`):
+The following software is included in the Dfam TE Tools container (version `1.3.1`):
 
 | | | |
 | -------------- | -------- | --- |
 | RepeatModeler  | 2.0.1    | <http://www.repeatmasker.org/RepeatModeler/>
-| RepeatMasker   | 4.1.2    | <http://www.repeatmasker.org/RMDownload.html>
+| RepeatMasker   | 4.1.2-p1 | <http://www.repeatmasker.org/RMDownload.html>
 | coseg          | 0.2.2    | <http://www.repeatmasker.org/COSEGDownload.html>
 | | | |
 | RMBlast        | 2.11.0   | <http://www.repeatmasker.org/RMBlast.html>

diff --git a/dfam-tetools.sh b/dfam-tetools.sh
@@ -44,7 +44,7 @@ programs are available, singularity is preferred."
 
 ## Parse command-line arguments ##
 
-container="dfam/tetools:1.3"
+container="dfam/tetools:1.3.1"
 use_docker=0
 use_singularity=0
 

diff --git a/getsrc.sh b/getsrc.sh
@@ -34,7 +34,7 @@ download https://github.com/oushujun/LTR_retriever/archive/v2.9.0.tar.gz LTR_ret
 download https://mafft.cbrc.jp/alignment/software/mafft-7.471-without-extensions-src.tgz
 download https://github.com/TravisWheelerLab/NINJA/archive/0.97-cluster_only.tar.gz NINJA-cluster.tar.gz
 download http://www.repeatmasker.org/coseg-0.2.2.tar.gz
-download http://www.repeatmasker.org/RepeatMasker/RepeatMasker-4.1.2.tar.gz
+download http://www.repeatmasker.org/RepeatMasker/RepeatMasker-4.1.2-p1.tar.gz
 download https://github.com/Dfam-consortium/RepeatModeler/archive/2.0.1.tar.gz RepeatModeler-2.0.1.tar.gz
 
 for tool in faToTwoBit twoBitInfo twoBitToFa; do

diff --git a/sha256sums.txt b/sha256sums.txt
@@ -7,6 +7,7 @@ e2d94f6179c33990a77fa9fdcefb842c8481b4c30833c9c12cbbe54cb3fdda73  LTR_retriever-
 60f8ec7bab80e00dbb24be65b8000312ffc98ff10eb72fc2219869d1dd382964  mafft-7.471-without-extensions-src.tgz
 b9b948c698efc3838e63817f732ead35c08debe1c0ae36b5c74df7d26ca4c4b6  NINJA-cluster.tar.gz
 699765fa49d18dbfac9f7a82ecd054464b468cb7521abe9c2bd8caccf08ee7d8  RECON-1.08.tar.gz
+4be54bf6c050422b211e24a797feb06fd7954c8b4ee6f3ece94cb6faaf6b0e96  RepeatMasker-4.1.2-p1.tar.gz
 bb85d30a85e3462eabf7b350b4be0331c322152a6c88faab45817346d70cfdb2  RepeatMasker-4.1.2.tar.gz
 628e7e1556865a86ed9d6a644c0c5487454c99fbcac21b68eae302fae7abb7ac  RepeatModeler-2.0.1.tar.gz
 31a44cf648d78356aec585ee5d3baf936d01eaba43aed382d9ac2d764e55b716  RepeatScout-1.0.6.tar.gz