release 1.85

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/).
 
+## 1.85 - 2023-5/09
+### Updated
+- RMBlast:  `2.13.0` -> `2.14.0`
+
 ## 1.8 - 2023-3/23
 ### Updated
 - RepeatMasker:  `4.1.4` -> `4.1.5`

Dockerfile

@@ -1,11 +1,6 @@
 # Dfam TE Tools container including RepeatMasker, RepeatModeler, coseg
 
-# Why debian:9? glibc, and probably other libraries, occasionally take
-# advantage of new kernel syscalls. Docker containers normally run with the
-# host machine's kernel. Debian 9 has an old enough glibc to not have many
-# features that would only work on newer machines, and the other packages are
-# new enough to compile all of these dependencies.
-FROM debian:9 AS builder
+FROM debian:10 AS builder
 
 RUN apt-get -y update && apt-get -y install \
     curl gcc g++ make zlib1g-dev libgomp1 \
@@ -14,8 +9,13 @@ RUN apt-get -y update && apt-get -y install \
     libfile-which-perl \
     libtext-soundex-perl \
     libjson-perl liburi-perl libwww-perl \
-    libdevel-size-perl
-
+    libdevel-size-perl \
+    aptitude && aptitude install -y ~pstandard ~prequired \
+    curl wget \
+    vim nano \
+    procps strace \
+    libpam-systemd-
+
 COPY src/* /opt/src/
 COPY sha256sums.txt /opt/src/
 WORKDIR /opt/src
@@ -25,8 +25,8 @@ RUN sha256sum -c sha256sums.txt
 # Extract RMBlast
 RUN cd /opt \
     && mkdir rmblast \
-    && tar --strip-components=1 -x -f src/rmblast-2.13.0+-x64-linux.tar.gz -C rmblast \
-    && rm src/rmblast-2.13.0+-x64-linux.tar.gz
+    && tar --strip-components=1 -x -f src/rmblast-2.14.0+-x64-linux.tar.gz -C rmblast \
+    && rm src/rmblast-2.14.0+-x64-linux.tar.gz
 
 # Compile HMMER
 RUN tar -x -f hmmer-3.3.2.tar.gz \
@@ -133,27 +133,8 @@ RUN cd /opt \
          -trf_dir=/opt \
          -ucsctools_dir=/opt/ucsc_tools
 
-FROM debian:9
-
-# Install dependencies and some basic utilities
-RUN apt-get -y update \
-    && apt-get -y install \
-        aptitude \
-        libgomp1 \
-        perl \
-        python3-h5py \
-        libfile-which-perl \
-        libtext-soundex-perl \
-        libjson-perl liburi-perl libwww-perl \
-        libdevel-size-perl \
-    && aptitude install -y ~pstandard ~prequired \
-        curl wget \
-        vim nano \
-        procps strace \
-        libpam-systemd-
-
-COPY --from=builder /opt /opt
+# COPY --from=builder /opt /opt
 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:/bin
+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

README.md

@@ -169,7 +169,7 @@ The following software is included in the Dfam TE Tools container (version `1.8`
 | RepeatMasker   | 4.1.5    | <http://www.repeatmasker.org/RMDownload.html>
 | coseg          | 0.2.2    | <http://www.repeatmasker.org/COSEGDownload.html>
 | | | |
-| RMBlast        | 2.13.0   | <http://www.repeatmasker.org/RMBlast.html>
+| RMBlast        | 2.14.0   | <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>

dfam-tetools.sh

@@ -31,7 +31,7 @@ programs are available, singularity is preferred."
 
 ## Parse command-line arguments ##
 
-container="dfam/tetools:1.8"
+container="dfam/tetools:1.85"
 use_docker=0
 use_singularity=0
 

getsrc.sh

@@ -23,7 +23,7 @@ download() {
 
 mkdir -p src
 
-download https://www.repeatmasker.org/rmblast/rmblast-2.13.0+-x64-linux.tar.gz
+download https://www.repeatmasker.org/rmblast/rmblast-2.14.0+-x64-linux.tar.gz
 download http://eddylab.org/software/hmmer/hmmer-3.3.2.tar.gz
 download https://github.com/Benson-Genomics-Lab/TRF/archive/v4.09.1.tar.gz trf-4.09.1.tar.gz
 download https://www.repeatmasker.org/RepeatScout-1.0.6.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
-afe23ceb279fd9f0f5d48c8112f5dff1ac6f1572f4da20492d9ac22e56427096  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
-4190916cea0c188af1de9a8dfac41c69eb6c8680aef46d48a2de7d3d1c13f9c2  RepeatMasker-4.1.5.tar.gz
-94aad46cc70911d48de3001836fc3165adb95b2b282b5c53ab0d1da98c27a6b6  RepeatModeler-2.0.4.tar.gz
-31a44cf648d78356aec585ee5d3baf936d01eaba43aed382d9ac2d764e55b716  RepeatScout-1.0.6.tar.gz
-164b09b63e2d5212d8d44750f6d0f32bacb2d65e52521cd84f29f3e1f2d75624  rmblast-2.13.0+-x64-linux.tar.gz
-516015b625473350c3d1c9b83cac86baea620c8418498ab64c0a67029c3fb28a  trf-4.09.1.tar.gz
-cb4eb5f3e41189a23fa381f70937821aa2044323ce1e78689cc5e05a5209e790  twoBitInfo
-e9a325b0acdb6cf5184bc53c3861b7484e5040342308f22da62a46d572346b85  twoBitToFa
+26172dba3040d1ae5c73ff0ac6c3be8c8e60cc49fc7379e434cdf9cb1e7415de *cd-hit-v4.8.1-2019-0228.tar.gz
+e666874cc602d6a03c45eb2f19dc53b2d95150c6aae83fea0842b7db1d157682 *coseg-0.2.2.tar.gz
+c7084ed5757979aa9521276762eaff78ebae977ed7cc40a3cdfc6f6961b41340 *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
+94aad46cc70911d48de3001836fc3165adb95b2b282b5c53ab0d1da98c27a6b6 *RepeatModeler-2.0.4.tar.gz
+d1d2c32d7343efae3735bc7769b56bc23dd8009c566b7d04f3c796083a7bdace *RepeatScout-1.0.6.tar.gz
+194a81d6189ae21fa80f6f605d412a5a7315d9145cccce7e7377147bf512d35f *rmblast-2.14.0+-x64-linux.tar.gz
+516015b625473350c3d1c9b83cac86baea620c8418498ab64c0a67029c3fb28a *trf-4.09.1.tar.gz
+eb1a6b4a264c12aa1a95b373eb213e3f1c5bd2b6163bbbc90bdc0eb0d3a1dfad *twoBitInfo
+bb3456ca804bbeb6e817263989cc18956c605afc3b31ef9df5a9108dab69cee5 *twoBitToFa