updgrade os to debian 12

CHANGELOG.md

@@ -7,6 +7,8 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/).
 ### Updated
 - RMBlast: `2.14.0` -> `2.14.1`
 - RepeatModeler: `2.0.4` -> `2.0.5`
+- genometools: `1.6.0` -> `1.6.4`
+- coseg: `0.2.2` -> `0.2.3`
 
 ## 1.85 - 2023-5/09
 ### Updated

Dockerfile

@@ -1,9 +1,13 @@
 # Dfam TE Tools container including RepeatMasker, RepeatModeler, coseg
 
-FROM debian:10 AS builder
+FROM debian:12 AS builder
 
 RUN apt-get -y update && apt-get -y install \
-    curl gcc g++ make zlib1g-dev libgomp1 \
+    gcc \
+    g++ \
+    make \
+    zlib1g-dev \
+    libgomp1 \
     perl \
     python3-h5py \
     libfile-which-perl \
@@ -18,6 +22,7 @@ RUN apt-get -y update && apt-get -y install \
 
 COPY src/* /opt/src/
 COPY sha256sums.txt /opt/src/
+COPY container_test.sh /opt/src/
 WORKDIR /opt/src
 
 RUN sha256sum -c sha256sums.txt
@@ -61,8 +66,8 @@ RUN tar -x -f cd-hit-v4.8.1-2019-0228.tar.gz \
     && make && mkdir /opt/cd-hit && PREFIX=/opt/cd-hit make install
 
 # Compile genometools (for ltrharvest)
-RUN tar -x -f gt-1.6.0.tar.gz \
-    && cd genometools-1.6.0 \
+RUN tar -x -f gt-1.6.4.tar.gz \
+    && cd genometools-1.6.4 \
     && make -j4 cairo=no && make cairo=no prefix=/opt/genometools install \
     && make cleanup
 
@@ -100,8 +105,11 @@ COPY LICENSE.ucsc /opt/ucsc_tools/LICENSE
 
 # Compile and configure coseg
 RUN cd /opt \
-    && tar -x -f src/coseg-0.2.2.tar.gz \
-    && cd coseg \
+    && mkdir coseg \
+    && tar -x -f src/coseg-0.2.3.tar.gz -C ./coseg \
+    && cd coseg/coseg-coseg-0.2.3 \
+    && mv * ../ \
+    && cd ../ \
     && sed -i 's@#!.*perl@#!/usr/bin/perl@' preprocessAlignments.pl runcoseg.pl refineConsSeqs.pl \
     && sed -i 's#use lib "/usr/local/RepeatMasker";#use lib "/opt/RepeatMasker";#' preprocessAlignments.pl \
     && make
@@ -138,3 +146,5 @@ RUN echo "PS1='(dfam-tetools \$(pwd))\\\$ '" >> /etc/bash.bashrc
 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
+
+RUN /opt/src/container_test.sh

README.md

@@ -167,15 +167,15 @@ The following software is included in the Dfam TE Tools container (version `1.86
 | -------------- | -------- | --- |
 | RepeatModeler  | 2.0.5    | <http://www.repeatmasker.org/RepeatModeler/>
 | RepeatMasker   | 4.1.5    | <http://www.repeatmasker.org/RMDownload.html>
-| coseg          | 0.2.2    | <http://www.repeatmasker.org/COSEGDownload.html>
+| coseg          | 0.2.3    | <http://www.repeatmasker.org/COSEGDownload.html>
 | | | |
 | RMBlast        | 2.14.1   | <http://www.repeatmasker.org/RMBlast.html>
 | HMMER          | 3.3.2    | <http://hmmer.org/>
 | TRF            | 4.09.1   | <https://github.com/Benson-Genomics-Lab/TRF> |
 | RepeatScout    | 1.0.6    | <http://www.repeatmasker.org/RepeatScout-1.0.6.tar.gz>
 | RECON          | 1.08     | <http://www.repeatmasker.org/RepeatModeler/RECON-1.08.tar.gz>
 | cd-hit         | 4.8.1    | <https://github.com/weizhongli/cdhit>
-| genometools    | 1.6.0    | <https://github.com/genometools/genometools>
+| genometools    | 1.6.4    | <https://github.com/genometools/genometools>
 | LTR\_retriever | 2.9.0    | <https://github.com/oushujun/LTR_retriever/>
 | MAFFT          | 7.471    |  <https://mafft.cbrc.jp/alignment/software/>
 | NINJA          | 0.97-cluster\_only | <https://github.com/TravisWheelerLab/NINJA>

container_test.sh

@@ -0,0 +1,10 @@
+#!/bin/sh
+
+set -eu
+
+declare -A tests=(
+    ["rmblast"]='/opt/rmblast/bin/rmblast -help'
+    ["other"]='placeholder'
+)
+echo "${tests[other]}"
+for test in "${!tests[@]}"; do echo "$test - ${tests[$test]}"; done

getsrc.sh

@@ -29,11 +29,12 @@ download https://github.com/Benson-Genomics-Lab/TRF/archive/v4.09.1.tar.gz trf-4
 download https://www.repeatmasker.org/RepeatScout-1.0.6.tar.gz
 download https://www.repeatmasker.org/RepeatModeler/RECON-1.08.tar.gz
 download https://github.com/weizhongli/cdhit/releases/download/V4.8.1/cd-hit-v4.8.1-2019-0228.tar.gz
-download https://github.com/genometools/genometools/archive/v1.6.0.tar.gz gt-1.6.0.tar.gz
+download https://github.com/genometools/genometools/archive/v1.6.4.tar.gz gt-1.6.4.tar.gz
 download https://github.com/oushujun/LTR_retriever/archive/v2.9.0.tar.gz LTR_retriever-2.9.0.tar.gz
 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/coseg-0.2.3.tar.gz
+download https://github.com/rmhubley/coseg/archive/refs/tags/coseg-0.2.3.tar.gz
 download https://www.repeatmasker.org/RepeatMasker/RepeatMasker-4.1.5.tar.gz
 download https://github.com/Dfam-consortium/RepeatModeler/archive/2.0.5.tar.gz RepeatModeler-2.0.5.tar.gz
 

sha256sums.txt

@@ -1,16 +1,16 @@
-26172dba3040d1ae5c73ff0ac6c3be8c8e60cc49fc7379e434cdf9cb1e7415de  cd-hit-v4.8.1-2019-0228.tar.gz
-e666874cc602d6a03c45eb2f19dc53b2d95150c6aae83fea0842b7db1d157682  coseg-0.2.2.tar.gz
-a2c6764c970666c975141e611b650ab4a2094f9d0f416825112f146268fd9d19  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
-16e07f9efd99adf15f4492b0e334df5ad4ea6ca38ddf62bdd180d257f2f4753f  RepeatMasker-4.1.5.tar.gz
-4c005ada7e88ff944116832349580a0dc3db762dc1c91235fa574b32ea9a8452  RepeatModeler-2.0.5.tar.gz
-d1d2c32d7343efae3735bc7769b56bc23dd8009c566b7d04f3c796083a7bdace  RepeatScout-1.0.6.tar.gz
-a5e19700282a3423481d6198db37d2d0bdf2c530b4fb7cef7f1aa2c92364baae  rmblast-2.14.1+-x64-linux.tar.gz
-516015b625473350c3d1c9b83cac86baea620c8418498ab64c0a67029c3fb28a  trf-4.09.1.tar.gz
-a543d943d73d75c40191f3d103d86eb75d7f1e2d6e8f1364a93f2dfc09d238ba  twoBitInfo
-92dd610bce8621d8b0951da6d428d65f138df068322e96b26cfe1840cb180dc6  twoBitToFa
+26172dba3040d1ae5c73ff0ac6c3be8c8e60cc49fc7379e434cdf9cb1e7415de *cd-hit-v4.8.1-2019-0228.tar.gz
+0c48fba155264db8a9e544689678c9f691fee511b74e0b5d227b827657555235 *coseg-0.2.3.tar.gz
+a2c6764c970666c975141e611b650ab4a2094f9d0f416825112f146268fd9d19 *faToTwoBit
+eda9cf3a5d63e5017f3c315c5700b0e308c08793d5795bc889350a536369a449 *gt-1.6.4.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
+16e07f9efd99adf15f4492b0e334df5ad4ea6ca38ddf62bdd180d257f2f4753f *RepeatMasker-4.1.5.tar.gz
+4c005ada7e88ff944116832349580a0dc3db762dc1c91235fa574b32ea9a8452 *RepeatModeler-2.0.5.tar.gz
+d1d2c32d7343efae3735bc7769b56bc23dd8009c566b7d04f3c796083a7bdace *RepeatScout-1.0.6.tar.gz
+a5e19700282a3423481d6198db37d2d0bdf2c530b4fb7cef7f1aa2c92364baae *rmblast-2.14.1+-x64-linux.tar.gz
+516015b625473350c3d1c9b83cac86baea620c8418498ab64c0a67029c3fb28a *trf-4.09.1.tar.gz
+a543d943d73d75c40191f3d103d86eb75d7f1e2d6e8f1364a93f2dfc09d238ba *twoBitInfo
+92dd610bce8621d8b0951da6d428d65f138df068322e96b26cfe1840cb180dc6 *twoBitToFa