diff --git a/CHANGELOG.md b/CHANGELOG.md index 4c0e14c..0bdf0ad 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/). +## 1.3.1 - 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 index 07b38d8..197b61f 100644 --- 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 index 255191d..620bdbe 100644 --- 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 | -| RepeatMasker | 4.1.2 | +| RepeatMasker | 4.1.2-p1 | | coseg | 0.2.2 | | | | | | RMBlast | 2.11.0 | diff --git a/dfam-tetools.sh b/dfam-tetools.sh index 56070e5..fe2d4cd 100755 --- 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 index d1ed5a4..b22a1d9 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 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 index 732701a..35583d4 100644 --- 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