ver 1.89.1

CHANGELOG.md

@@ -2,6 +2,11 @@
 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/).
+
+## 1.89.1
+### Updated
+- RepeatMasker: `4.1.7` -> `4.1.7-p1`
+
 ## 1.89
 ### Updated
 - RepeatMasker: `4.1.6` -> `4.1.7`

Dockerfile

@@ -128,7 +128,7 @@ RUN cd /opt \
 # With Minimal TE Library
 #   - Also with full Dfam curated RepeatMasker.lib for RepeatClassifier
 RUN cd /opt \
-    && tar -x -f src/RepeatMasker-4.1.7.tar.gz \
+    && tar -x -f src/RepeatMasker-4.1.7-p1.tar.gz \
     && chmod a+w RepeatMasker/Libraries \
     && chmod a+w RepeatMasker/Libraries/famdb \
     && cd RepeatMasker \
@@ -184,7 +184,5 @@ 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
 
-COPY container_test.sh /opt/
-RUN chmod 701 /opt/container_test.sh
-RUN /opt/container_test.sh | echo
-RUN rm -r /opt/src
+RUN chmod +x /opt/ucsc_tools/* \
+    && rm -r /opt/src

README.md

@@ -213,12 +213,12 @@ docker buildx build --platform=linux/amd64,linux/arm64 --output=type=registry -t
 
 ## Included software
 
-The following software is included in the Dfam TE Tools container (version `1.89`):
+The following software is included in the Dfam TE Tools container (version `1.89.1`):
 
 | | | |
 | -------------- | -------- | --- |
 | RepeatModeler  | 2.0.5    | <http://www.repeatmasker.org/RepeatModeler/>
-| RepeatMasker   | 4.1.7    | <http://www.repeatmasker.org/RMDownload.html>
+| RepeatMasker   | 4.1.7-p1 | <http://www.repeatmasker.org/RMDownload.html>
 | coseg          | 0.2.3    | <http://www.repeatmasker.org/COSEGDownload.html>
 | | | |
 | RMBlast        | 2.14.1   | <http://www.repeatmasker.org/RMBlast.html>

dfam-tetools.sh

@@ -31,7 +31,7 @@ programs are available, singularity is preferred."
 
 ## Parse command-line arguments ##
 
-container="dfam/tetools:1.89"
+container="dfam/tetools:1.89.1"
 use_docker=0
 use_singularity=0
 use_lib=0

getsrc.sh

@@ -37,7 +37,7 @@ download https://github.com/TravisWheelerLab/NINJA/archive/1.00-cluster_only.tar
 download https://github.com/rmhubley/coseg/archive/refs/tags/coseg-0.2.3.tar.gz
 # download https://www.dfam.org/releases/Dfam_3.8/families/FamDB/dfam38_full.0.h5.gz
 download https://www.dfam.org/releases/Dfam_3.8/families/Dfam-RepeatMasker.lib.gz
-# download http://www.repeatmasker.org/RepeatMasker/RepeatMasker-4.1.7.tar.gz
+download http://www.repeatmasker.org/RepeatMasker/RepeatMasker-4.1.7-p1.tar.gz
 download https://github.com/Dfam-consortium/RepeatModeler/archive/2.0.5.tar.gz RepeatModeler-2.0.5.tar.gz
 # download https://github.com/zhangrengang/TEsorter/archive/v1.4.6.tar.gz TEsorter-1.4.6.tar.gz
 

sha256sums.txt

@@ -1,18 +1,21 @@
 26172dba3040d1ae5c73ff0ac6c3be8c8e60cc49fc7379e434cdf9cb1e7415de  cd-hit-v4.8.1-2019-0228.tar.gz
 0c48fba155264db8a9e544689678c9f691fee511b74e0b5d227b827657555235  coseg-0.2.3.tar.gz
-b53e09a3db2d01943c4167d9b457addf9194988c298f4ce600236da7e3fc3dfd  dfam38_full.0.h5.gz
 31242db2d262305ebdf52c5c7a93743889bdb0f75253750964a0db9e8aa27711  Dfam-RepeatMasker.lib.gz
-d9897ad14695b701e3818c494b2048aa13d089d9b0a7a8b20170d9f87b67e13f  faToTwoBit
+bcc8cbe3c0e3b1eb6861cfed4b8495b2b1e28f922623a6bf57f389b76037538e  faToTwoBit_arm64
+d9897ad14695b701e3818c494b2048aa13d089d9b0a7a8b20170d9f87b67e13f  faToTwoBit_x86
 eda9cf3a5d63e5017f3c315c5700b0e308c08793d5795bc889350a536369a449  gt-1.6.4.tar.gz
 ca70d94fd0cf271bd7063423aabb116d42de533117343a9b27a65c17ff06fbf3  hmmer-3.4.tar.gz
 e2d94f6179c33990a77fa9fdcefb842c8481b4c30833c9c12cbbe54cb3fdda73  LTR_retriever-2.9.0.tar.gz
 60f8ec7bab80e00dbb24be65b8000312ffc98ff10eb72fc2219869d1dd382964  mafft-7.471-without-extensions-src.tgz
 3138d74522df9531e7573cf801bacc6a36768ae3c606a4b046cbd4c1acd9ca4c  NINJA-cluster.tar.gz
 699765fa49d18dbfac9f7a82ecd054464b468cb7521abe9c2bd8caccf08ee7d8  RECON-1.08.tar.gz
-f39d9aec38383dc87e6ebeb27b5a229dc1c41049dc99ba0ca906e6017f8985f9  RepeatMasker-4.1.7.tar.gz
+15222b39178f19c116282437190b64c5ba68f62b0f2044b3bbcbda5e02748993  RepeatMasker-4.1.7-p1.tar.gz
 4c005ada7e88ff944116832349580a0dc3db762dc1c91235fa574b32ea9a8452  RepeatModeler-2.0.5.tar.gz
 d1d2c32d7343efae3735bc7769b56bc23dd8009c566b7d04f3c796083a7bdace  RepeatScout-1.0.6.tar.gz
+fdaf9eb9e87c2bf34605d23b5a0711999306dd37980ae01662f6bed9ce5280c3  rmblast-2.14.1+-arm64-macosx.tar.gz
 a5e19700282a3423481d6198db37d2d0bdf2c530b4fb7cef7f1aa2c92364baae  rmblast-2.14.1+-x64-linux.tar.gz
 516015b625473350c3d1c9b83cac86baea620c8418498ab64c0a67029c3fb28a  trf-4.09.1.tar.gz
-7915d9c905bca42f6de00134ea052db898b098e34d001c3ea4ad2a3c528a1cf1  twoBitInfo
-a54b36631a280ba1cb3fb88ce8ebbd520d918468648dfce5569a95ba133bfcce  twoBitToFa
+803f1638e933e71aed707e60767a0a35fd1310c9459b438dc03819befe535a08  twoBitInfo_arm64
+7915d9c905bca42f6de00134ea052db898b098e34d001c3ea4ad2a3c528a1cf1  twoBitInfo_x86
+24dc672d0773553165a5444ab8182f19cc2c811ff5ad805107fab5144c678910  twoBitToFa_arm64
+a54b36631a280ba1cb3fb88ce8ebbd520d918468648dfce5569a95ba133bfcce  twoBitToFa_x86