From 733d0193756ffd85022df5997301264286e8249a Mon Sep 17 00:00:00 2001 From: Anthony Gray Date: Thu, 23 Mar 2023 16:19:02 -0700 Subject: [PATCH] update repeatmasker to 4.1.5 --- CHANGELOG.md | 4 ++++ Dockerfile | 4 ++-- README.md | 4 ++-- dfam-tetools.sh | 2 +- getsrc.sh | 2 +- sha256sums.txt | 32 ++++++++++++++++---------------- 6 files changed, 26 insertions(+), 22 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index b4eca71..2784e77 100644 --- 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/). +## 1.8 - 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` diff --git a/Dockerfile b/Dockerfile index e19c14e..4f7e123 100644 --- a/Dockerfile +++ b/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 \ diff --git a/README.md b/README.md index 01258e1..5c24792 100644 --- a/README.md +++ b/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 | -| RepeatMasker | 4.1.4 | +| RepeatMasker | 4.1.5 | | coseg | 0.2.2 | | | | | | RMBlast | 2.13.0 | diff --git a/dfam-tetools.sh b/dfam-tetools.sh index 2f1052c..2365ede 100755 --- a/dfam-tetools.sh +++ b/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 diff --git a/getsrc.sh b/getsrc.sh index 37e22a5..b3cd712 100755 --- 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 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. diff --git a/sha256sums.txt b/sha256sums.txt index 1f3126f..255f0c2 100644 --- a/sha256sums.txt +++ b/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