From 1e6201aee46ba74cd62b98b73f95f670fdd49054 Mon Sep 17 00:00:00 2001 From: asgray Date: Fri, 13 Sep 2024 12:34:20 -0700 Subject: [PATCH] ver 1.89.1 --- CHANGELOG.md | 5 +++++ Dockerfile | 8 +++----- README.md | 4 ++-- dfam-tetools.sh | 2 +- getsrc.sh | 2 +- sha256sums.txt | 13 ++++++++----- 6 files changed, 20 insertions(+), 14 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 38f234d..4b71345 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -2,6 +2,11 @@ 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/). + +## 1.89.1 +### Updated +- RepeatMasker: `4.1.7` -> `4.1.7-p1` + ## 1.89 ### Updated - RepeatMasker: `4.1.6` -> `4.1.7` diff --git a/Dockerfile b/Dockerfile index ea9904e..2a3acc1 100644 --- a/Dockerfile +++ b/Dockerfile @@ -128,7 +128,7 @@ RUN cd /opt \ # With Minimal TE Library # - Also with full Dfam curated RepeatMasker.lib for RepeatClassifier RUN cd /opt \ - && tar -x -f src/RepeatMasker-4.1.7.tar.gz \ + && tar -x -f src/RepeatMasker-4.1.7-p1.tar.gz \ && chmod a+w RepeatMasker/Libraries \ && chmod a+w RepeatMasker/Libraries/famdb \ && cd RepeatMasker \ @@ -184,7 +184,5 @@ ENV LANG=C ENV PYTHONIOENCODING=utf8 ENV PATH=/opt/RepeatMasker:/opt/RepeatMasker/util:/opt/RepeatModeler:/opt/RepeatModeler/util:/opt/coseg:/opt/ucsc_tools:/opt:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/opt/rmblast/bin:/bin -COPY container_test.sh /opt/ -RUN chmod 701 /opt/container_test.sh -RUN /opt/container_test.sh | echo -RUN rm -r /opt/src +RUN chmod +x /opt/ucsc_tools/* \ + && rm -r /opt/src \ No newline at end of file diff --git a/README.md b/README.md index 4975704..66df3e2 100644 --- a/README.md +++ b/README.md @@ -213,12 +213,12 @@ docker buildx build --platform=linux/amd64,linux/arm64 --output=type=registry -t ## Included software -The following software is included in the Dfam TE Tools container (version `1.89`): +The following software is included in the Dfam TE Tools container (version `1.89.1`): | | | | | -------------- | -------- | --- | | RepeatModeler | 2.0.5 | -| RepeatMasker | 4.1.7 | +| RepeatMasker | 4.1.7-p1 | | coseg | 0.2.3 | | | | | | RMBlast | 2.14.1 | diff --git a/dfam-tetools.sh b/dfam-tetools.sh index 6953179..813645a 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:1.89" +container="dfam/tetools:1.89.1" use_docker=0 use_singularity=0 use_lib=0 diff --git a/getsrc.sh b/getsrc.sh index 8be2898..4458168 100755 --- a/getsrc.sh +++ b/getsrc.sh @@ -37,7 +37,7 @@ download https://github.com/TravisWheelerLab/NINJA/archive/1.00-cluster_only.tar download https://github.com/rmhubley/coseg/archive/refs/tags/coseg-0.2.3.tar.gz # download https://www.dfam.org/releases/Dfam_3.8/families/FamDB/dfam38_full.0.h5.gz download https://www.dfam.org/releases/Dfam_3.8/families/Dfam-RepeatMasker.lib.gz -# download http://www.repeatmasker.org/RepeatMasker/RepeatMasker-4.1.7.tar.gz +download http://www.repeatmasker.org/RepeatMasker/RepeatMasker-4.1.7-p1.tar.gz download https://github.com/Dfam-consortium/RepeatModeler/archive/2.0.5.tar.gz RepeatModeler-2.0.5.tar.gz # download https://github.com/zhangrengang/TEsorter/archive/v1.4.6.tar.gz TEsorter-1.4.6.tar.gz diff --git a/sha256sums.txt b/sha256sums.txt index 6a3c772..5e52859 100644 --- a/sha256sums.txt +++ b/sha256sums.txt @@ -1,18 +1,21 @@ 26172dba3040d1ae5c73ff0ac6c3be8c8e60cc49fc7379e434cdf9cb1e7415de cd-hit-v4.8.1-2019-0228.tar.gz 0c48fba155264db8a9e544689678c9f691fee511b74e0b5d227b827657555235 coseg-0.2.3.tar.gz -b53e09a3db2d01943c4167d9b457addf9194988c298f4ce600236da7e3fc3dfd dfam38_full.0.h5.gz 31242db2d262305ebdf52c5c7a93743889bdb0f75253750964a0db9e8aa27711 Dfam-RepeatMasker.lib.gz -d9897ad14695b701e3818c494b2048aa13d089d9b0a7a8b20170d9f87b67e13f faToTwoBit +bcc8cbe3c0e3b1eb6861cfed4b8495b2b1e28f922623a6bf57f389b76037538e faToTwoBit_arm64 +d9897ad14695b701e3818c494b2048aa13d089d9b0a7a8b20170d9f87b67e13f faToTwoBit_x86 eda9cf3a5d63e5017f3c315c5700b0e308c08793d5795bc889350a536369a449 gt-1.6.4.tar.gz ca70d94fd0cf271bd7063423aabb116d42de533117343a9b27a65c17ff06fbf3 hmmer-3.4.tar.gz e2d94f6179c33990a77fa9fdcefb842c8481b4c30833c9c12cbbe54cb3fdda73 LTR_retriever-2.9.0.tar.gz 60f8ec7bab80e00dbb24be65b8000312ffc98ff10eb72fc2219869d1dd382964 mafft-7.471-without-extensions-src.tgz 3138d74522df9531e7573cf801bacc6a36768ae3c606a4b046cbd4c1acd9ca4c NINJA-cluster.tar.gz 699765fa49d18dbfac9f7a82ecd054464b468cb7521abe9c2bd8caccf08ee7d8 RECON-1.08.tar.gz -f39d9aec38383dc87e6ebeb27b5a229dc1c41049dc99ba0ca906e6017f8985f9 RepeatMasker-4.1.7.tar.gz +15222b39178f19c116282437190b64c5ba68f62b0f2044b3bbcbda5e02748993 RepeatMasker-4.1.7-p1.tar.gz 4c005ada7e88ff944116832349580a0dc3db762dc1c91235fa574b32ea9a8452 RepeatModeler-2.0.5.tar.gz d1d2c32d7343efae3735bc7769b56bc23dd8009c566b7d04f3c796083a7bdace RepeatScout-1.0.6.tar.gz +fdaf9eb9e87c2bf34605d23b5a0711999306dd37980ae01662f6bed9ce5280c3 rmblast-2.14.1+-arm64-macosx.tar.gz a5e19700282a3423481d6198db37d2d0bdf2c530b4fb7cef7f1aa2c92364baae rmblast-2.14.1+-x64-linux.tar.gz 516015b625473350c3d1c9b83cac86baea620c8418498ab64c0a67029c3fb28a trf-4.09.1.tar.gz -7915d9c905bca42f6de00134ea052db898b098e34d001c3ea4ad2a3c528a1cf1 twoBitInfo -a54b36631a280ba1cb3fb88ce8ebbd520d918468648dfce5569a95ba133bfcce twoBitToFa +803f1638e933e71aed707e60767a0a35fd1310c9459b438dc03819befe535a08 twoBitInfo_arm64 +7915d9c905bca42f6de00134ea052db898b098e34d001c3ea4ad2a3c528a1cf1 twoBitInfo_x86 +24dc672d0773553165a5444ab8182f19cc2c811ff5ad805107fab5144c678910 twoBitToFa_arm64 +a54b36631a280ba1cb3fb88ce8ebbd520d918468648dfce5569a95ba133bfcce twoBitToFa_x86