version 1.86

CHANGELOG.md

@@ -3,6 +3,11 @@ 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/).
 
+## 1.86 - 2023-10/09
+### Updated
+- RMBlast: `2.14.0` -> `2.14.1`
+- RepeatModeler: `2.0.4` -> `2.0.5`
+
 ## 1.85 - 2023-5/09
 ### Updated
 - RMBlast:  `2.13.0` -> `2.14.0`

Dockerfile

@@ -25,8 +25,8 @@ RUN sha256sum -c sha256sums.txt
 # Extract RMBlast
 RUN cd /opt \
     && mkdir rmblast \
-    && tar --strip-components=1 -x -f src/rmblast-2.14.0+-x64-linux.tar.gz -C rmblast \
-    && rm src/rmblast-2.14.0+-x64-linux.tar.gz
+    && tar --strip-components=1 -x -f src/rmblast-2.14.1+-x64-linux.tar.gz -C rmblast \
+    && rm src/rmblast-2.14.1+-x64-linux.tar.gz
 
 # Compile HMMER
 RUN tar -x -f hmmer-3.3.2.tar.gz \
@@ -121,8 +121,8 @@ RUN cd /opt \
 
 # Configure RepeatModeler
 RUN cd /opt \
-    && tar -x -f src/RepeatModeler-2.0.4.tar.gz \
-    && mv RepeatModeler-2.0.4 RepeatModeler \
+    && tar -x -f src/RepeatModeler-2.0.5.tar.gz \
+    && mv RepeatModeler-2.0.5 RepeatModeler \
     && cd RepeatModeler \
     && perl configure \
          -cdhit_dir=/opt/cd-hit -genometools_dir=/opt/genometools/bin \

README.md

@@ -161,15 +161,15 @@ singularity build dfam-tetools.sif dfam-tetools.def
 
 ## Included software
 
-The following software is included in the Dfam TE Tools container (version `1.8`):
+The following software is included in the Dfam TE Tools container (version `1.86`):
 
 | | | |
 | -------------- | -------- | --- |
-| RepeatModeler  | 2.0.4    | <http://www.repeatmasker.org/RepeatModeler/>
+| 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>
 | | | |
-| RMBlast        | 2.14.0   | <http://www.repeatmasker.org/RMBlast.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>

dfam-tetools.sh

@@ -31,7 +31,7 @@ programs are available, singularity is preferred."
 
 ## Parse command-line arguments ##
 
-container="dfam/tetools:1.85"
+container="dfam/tetools:1.86"
 use_docker=0
 use_singularity=0
 

getsrc.sh

@@ -23,7 +23,7 @@ download() {
 
 mkdir -p src
 
-download https://www.repeatmasker.org/rmblast/rmblast-2.14.0+-x64-linux.tar.gz
+download https://www.repeatmasker.org/rmblast/rmblast-2.14.1+-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
@@ -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-4.1.5.tar.gz
-download https://github.com/Dfam-consortium/RepeatModeler/archive/2.0.4.tar.gz RepeatModeler-2.0.4.tar.gz
+download https://github.com/Dfam-consortium/RepeatModeler/archive/2.0.5.tar.gz RepeatModeler-2.0.5.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'
@@ -49,4 +49,4 @@ cd ./src
 sha256sum -b * > sha256sums.txt
 cd ..
 cp ./src/sha256sums.txt sha256sums.txt
-rm ./src/sha256sums.txt 
+rm ./src/sha256sums.txt 

sha256sums.txt

@@ -1,16 +1,16 @@
-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
+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