diff --git a/CHANGELOG.md b/CHANGELOG.md index 479cc8b..f48427d 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/). +## Unreleased +### Updated +- RepeatModeler: `2.0.2a` -> `2.0.3` + ## 1.4 - 2021-05-03 ### Added - Installed `ps` in the container, for compatibility with Nextflow tracing/metrics diff --git a/Dockerfile b/Dockerfile index 0335759..fe95d23 100644 --- a/Dockerfile +++ b/Dockerfile @@ -13,7 +13,8 @@ RUN apt-get -y update && apt-get -y install \ python3-h5py \ libfile-which-perl \ libtext-soundex-perl \ - libjson-perl liburi-perl libwww-perl + libjson-perl liburi-perl libwww-perl \ + libdevel-size-perl COPY src/* /opt/src/ COPY sha256sums.txt /opt/src/ @@ -120,8 +121,8 @@ RUN cd /opt \ # Configure RepeatModeler RUN cd /opt \ - && tar -x -f src/RepeatModeler-2.0.2a.tar.gz \ - && mv RepeatModeler-2.0.2a RepeatModeler \ + && tar -x -f src/RepeatModeler-2.0.3.tar.gz \ + && mv RepeatModeler-2.0.3 RepeatModeler \ && cd RepeatModeler \ && perl configure \ -cdhit_dir=/opt/cd-hit -genometools_dir=/opt/genometools/bin \ @@ -129,7 +130,7 @@ RUN cd /opt \ -ninja_dir=/opt/NINJA/NINJA -recon_dir=/opt/RECON/bin \ -repeatmasker_dir=/opt/RepeatMasker \ -rmblast_dir=/opt/rmblast/bin -rscout_dir=/opt/RepeatScout \ - -trf_prgm=/opt/trf \ + -trf_dir=/opt \ -ucsctools_dir=/opt/ucsc_tools FROM debian:9 diff --git a/README.md b/README.md index 3fcc4e9..9592ae4 100644 --- a/README.md +++ b/README.md @@ -161,11 +161,11 @@ singularity build dfam-tetools.sif dfam-tetools.def ## Included software -The following software is included in the Dfam TE Tools container (version `1.4`): +The following software is included in the Dfam TE Tools container (version ``): | | | | | -------------- | -------- | --- | -| RepeatModeler | 2.0.2 | +| RepeatModeler | 2.0.3 | | RepeatMasker | 4.1.2-p1 | | coseg | 0.2.2 | | | | | diff --git a/getsrc.sh b/getsrc.sh index 2fd06d8..6b06336 100755 --- a/getsrc.sh +++ b/getsrc.sh @@ -35,7 +35,7 @@ download https://mafft.cbrc.jp/alignment/software/mafft-7.471-without-extensions 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-4.1.2-p1.tar.gz -download https://github.com/Dfam-consortium/RepeatModeler/archive/2.0.2a.tar.gz RepeatModeler-2.0.2a.tar.gz +download https://github.com/Dfam-consortium/RepeatModeler/archive/2.0.3.tar.gz RepeatModeler-2.0.3.tar.gz # TODO: /exe/ only includes binaries of the "latest" version at the time of download. # The version listed in README.md is obtained by running 'strings src/faToTwoBit | grep kent' diff --git a/sha256sums.txt b/sha256sums.txt index fdb9bdd..8422927 100644 --- a/sha256sums.txt +++ b/sha256sums.txt @@ -8,7 +8,7 @@ e2d94f6179c33990a77fa9fdcefb842c8481b4c30833c9c12cbbe54cb3fdda73 LTR_retriever- b9b948c698efc3838e63817f732ead35c08debe1c0ae36b5c74df7d26ca4c4b6 NINJA-cluster.tar.gz 699765fa49d18dbfac9f7a82ecd054464b468cb7521abe9c2bd8caccf08ee7d8 RECON-1.08.tar.gz 4be54bf6c050422b211e24a797feb06fd7954c8b4ee6f3ece94cb6faaf6b0e96 RepeatMasker-4.1.2-p1.tar.gz -8a9d69c8d7afbfb07f8bb6560c5f2fd35e61e5e7ccd01361e4f9a63f4ef3e50c RepeatModeler-2.0.2a.tar.gz +063bb8ab6b9f4bf18458504f6f90c0022ef5a5aebf2176f78f87f9e69faf7408 RepeatModeler-2.0.3.tar.gz 31a44cf648d78356aec585ee5d3baf936d01eaba43aed382d9ac2d764e55b716 RepeatScout-1.0.6.tar.gz 3e0a37fd6ec01a4c02acbf161e6d517725a5af783b610da5c7139066f0f1e6df rmblast-2.11.0+-x64-linux.tar.gz 516015b625473350c3d1c9b83cac86baea620c8418498ab64c0a67029c3fb28a trf-4.09.1.tar.gz