update repeatmasker to 4.1.5

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/).
 
+## 1.8 - 2023-3/23
+### Updated
+- RepeatMasker:  `4.1.4` -> `4.1.5`
+
 ## 1.7 - 2022-11/29
 ### Updated
 - RepeatMasker:  `4.1.3-p1` -> `4.1.4`

Dockerfile

@@ -108,7 +108,7 @@ RUN cd /opt \
 
 # Configure RepeatMasker
 RUN cd /opt \
-    && tar -x -f src/RepeatMasker-4.1.4.tar.gz \
+    && tar -x -f src/RepeatMasker-4.1.5.tar.gz \
     && chmod a+w RepeatMasker/Libraries \
     && cd RepeatMasker \
     && perl configure \
@@ -117,7 +117,7 @@ RUN cd /opt \
         -libdir=/opt/RepeatMasker/Libraries \
         -trf_prgm=/opt/trf \
         -default_search_engine=rmblast \
-    && cd .. && rm src/RepeatMasker-4.1.4.tar.gz
+    && cd .. && rm src/RepeatMasker-4.1.5.tar.gz
 
 # Configure RepeatModeler
 RUN cd /opt \

README.md

@@ -161,12 +161,12 @@ singularity build dfam-tetools.sif dfam-tetools.def
 
 ## Included software
 
-The following software is included in the Dfam TE Tools container (version `1.7`):
+The following software is included in the Dfam TE Tools container (version `1.8`):
 
 | | | |
 | -------------- | -------- | --- |
 | RepeatModeler  | 2.0.4    | <http://www.repeatmasker.org/RepeatModeler/>
-| RepeatMasker   | 4.1.4    | <http://www.repeatmasker.org/RMDownload.html>
+| RepeatMasker   | 4.1.5    | <http://www.repeatmasker.org/RMDownload.html>
 | coseg          | 0.2.2    | <http://www.repeatmasker.org/COSEGDownload.html>
 | | | |
 | RMBlast        | 2.13.0   | <http://www.repeatmasker.org/RMBlast.html>

dfam-tetools.sh

@@ -31,7 +31,7 @@ programs are available, singularity is preferred."
 
 ## Parse command-line arguments ##
 
-container="dfam/tetools:1.7"
+container="dfam/tetools:1.8"
 use_docker=0
 use_singularity=0
 

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 https://www.repeatmasker.org/coseg-0.2.2.tar.gz
-download https://www.repeatmasker.org/RepeatMasker/RepeatMasker-4.1.4.tar.gz
+download https://www.repeatmasker.org/RepeatMasker/RepeatMasker-4.1.5.tar.gz
 download https://github.com/Dfam-consortium/RepeatModeler/archive/2.0.4.tar.gz RepeatModeler-2.0.4.tar.gz
 
 # TODO: /exe/ only includes binaries of the "latest" version at the time of download.

sha256sums.txt

@@ -1,16 +1,16 @@
-26172dba3040d1ae5c73ff0ac6c3be8c8e60cc49fc7379e434cdf9cb1e7415de *cd-hit-v4.8.1-2019-0228.tar.gz
-e666874cc602d6a03c45eb2f19dc53b2d95150c6aae83fea0842b7db1d157682 *coseg-0.2.2.tar.gz
-527204e1c308f56b1f0a58b1053eb53dda1c0f8915f30d0e646e869678fafcdf *faToTwoBit
-d59dbf5bc6151b40ec6e53abfb3fa9f50136a054448759278a8c862e288cd3c9 *gt-1.6.0.tar.gz
-92fee9b5efe37a5276352d3502775e7c46e9f7a0ee45a331eacb2a0cac713c69 *hmmer-3.3.2.tar.gz
-e2d94f6179c33990a77fa9fdcefb842c8481b4c30833c9c12cbbe54cb3fdda73 *LTR_retriever-2.9.0.tar.gz
-60f8ec7bab80e00dbb24be65b8000312ffc98ff10eb72fc2219869d1dd382964 *mafft-7.471-without-extensions-src.tgz
-b9b948c698efc3838e63817f732ead35c08debe1c0ae36b5c74df7d26ca4c4b6 *NINJA-cluster.tar.gz
-699765fa49d18dbfac9f7a82ecd054464b468cb7521abe9c2bd8caccf08ee7d8 *RECON-1.08.tar.gz
-d7af5f49b7ecc5fb90e66956c85877220ec461f6e4d54e06a5996bb2fd6b63fa *RepeatMasker-4.1.4.tar.gz
-94aad46cc70911d48de3001836fc3165adb95b2b282b5c53ab0d1da98c27a6b6 *RepeatModeler-2.0.4.tar.gz
-31a44cf648d78356aec585ee5d3baf936d01eaba43aed382d9ac2d764e55b716 *RepeatScout-1.0.6.tar.gz
-164b09b63e2d5212d8d44750f6d0f32bacb2d65e52521cd84f29f3e1f2d75624 *rmblast-2.13.0+-x64-linux.tar.gz
-516015b625473350c3d1c9b83cac86baea620c8418498ab64c0a67029c3fb28a *trf-4.09.1.tar.gz
-373041b91af6fbc96e5aed055afdbadde9e6cbb8ab6792f6a1c01e8e1ede8289 *twoBitInfo
-fd7d063ecbfaaf924c8cf7a7da9f4f7a7c63013acb2f763474d2f6f8718c835e *twoBitToFa
+26172dba3040d1ae5c73ff0ac6c3be8c8e60cc49fc7379e434cdf9cb1e7415de  cd-hit-v4.8.1-2019-0228.tar.gz
+e666874cc602d6a03c45eb2f19dc53b2d95150c6aae83fea0842b7db1d157682  coseg-0.2.2.tar.gz
+afe23ceb279fd9f0f5d48c8112f5dff1ac6f1572f4da20492d9ac22e56427096  faToTwoBit
+d59dbf5bc6151b40ec6e53abfb3fa9f50136a054448759278a8c862e288cd3c9  gt-1.6.0.tar.gz
+92fee9b5efe37a5276352d3502775e7c46e9f7a0ee45a331eacb2a0cac713c69  hmmer-3.3.2.tar.gz
+e2d94f6179c33990a77fa9fdcefb842c8481b4c30833c9c12cbbe54cb3fdda73  LTR_retriever-2.9.0.tar.gz
+60f8ec7bab80e00dbb24be65b8000312ffc98ff10eb72fc2219869d1dd382964  mafft-7.471-without-extensions-src.tgz
+b9b948c698efc3838e63817f732ead35c08debe1c0ae36b5c74df7d26ca4c4b6  NINJA-cluster.tar.gz
+699765fa49d18dbfac9f7a82ecd054464b468cb7521abe9c2bd8caccf08ee7d8  RECON-1.08.tar.gz
+4190916cea0c188af1de9a8dfac41c69eb6c8680aef46d48a2de7d3d1c13f9c2  RepeatMasker-4.1.5.tar.gz
+94aad46cc70911d48de3001836fc3165adb95b2b282b5c53ab0d1da98c27a6b6  RepeatModeler-2.0.4.tar.gz
+31a44cf648d78356aec585ee5d3baf936d01eaba43aed382d9ac2d764e55b716  RepeatScout-1.0.6.tar.gz
+164b09b63e2d5212d8d44750f6d0f32bacb2d65e52521cd84f29f3e1f2d75624  rmblast-2.13.0+-x64-linux.tar.gz
+516015b625473350c3d1c9b83cac86baea620c8418498ab64c0a67029c3fb28a  trf-4.09.1.tar.gz
+cb4eb5f3e41189a23fa381f70937821aa2044323ce1e78689cc5e05a5209e790  twoBitInfo
+e9a325b0acdb6cf5184bc53c3861b7484e5040342308f22da62a46d572346b85  twoBitToFa