update: RepeatModeler to 2.0.3

Dfam-consortium · Feb 9, 2022 · dbba1bc · dbba1bc
1 parent 8875fe1
commit dbba1bc
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Showing 5 changed files with 13 additions and 8 deletions.
diff --git 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
@@ -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/
@@ -120,16 +121,16 @@ 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 \
          -ltr_retriever_dir=/opt/LTR_retriever -mafft_dir=/opt/mafft/bin \
          -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
@@ -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 `<unreleased>`):
 
 | | | |
 | -------------- | -------- | --- |
-| RepeatModeler  | 2.0.2    | <http://www.repeatmasker.org/RepeatModeler/>
+| RepeatModeler  | 2.0.3    | <http://www.repeatmasker.org/RepeatModeler/>
 | RepeatMasker   | 4.1.2-p1 | <http://www.repeatmasker.org/RMDownload.html>
 | coseg          | 0.2.2    | <http://www.repeatmasker.org/COSEGDownload.html>
 | | | |

diff --git 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
@@ -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