ver 1.90

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/).
 
+## 1.90
+### Updated
+- RepeatModeler: `2.0.5` -> `2.0.6`
+- RepeatScout: `1.0.6` -> `1.0.7`
+
 ## 1.89.1
 ### Updated
 - RepeatMasker: `4.1.7` -> `4.1.7-p1`

Dockerfile

@@ -58,10 +58,11 @@ RUN tar -x -f trf-4.09.1.tar.gz \
     && cd .. && rm -r build
 
 # Compile RepeatScout
-RUN tar -x -f RepeatScout-1.0.6.tar.gz \
-    && cd RepeatScout-1.0.6 \
+RUN tar -x -f RepeatScout-1.0.7.tar.gz \
+    && cd RepeatScout-1.0.7 \
+    && mv README.md README \
     && sed -i 's#^INSTDIR =.*#INSTDIR = /opt/RepeatScout#' Makefile \
-    && make && make install
+    && make install
 
 # Compile and configure RECON
 RUN tar -x -f RECON-1.08.tar.gz \
@@ -176,8 +177,8 @@ COPY tetoolsDfamUpdate.pl /opt/RepeatMasker/tetoolsDfamUpdate.pl
 
 # Configure RepeatModeler
 RUN cd /opt \
-    && tar -x -f src/RepeatModeler-2.0.5.tar.gz \
-    && mv RepeatModeler-2.0.5 RepeatModeler \
+    && tar -x -f src/RepeatModeler-2.0.6.tar.gz \
+    && mv RepeatModeler-2.0.6 RepeatModeler \
     && cd RepeatModeler \
     && perl configure \
          -cdhit_dir=/opt/cd-hit -genometools_dir=/opt/genometools/bin \

README.md

@@ -213,18 +213,18 @@ 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 `1.89.1`):
+The following software is included in the Dfam TE Tools container (version `1.90`):
 
 | | | |
 | -------------- | -------- | --- |
-| RepeatModeler  | 2.0.5    | <http://www.repeatmasker.org/RepeatModeler/>
+| RepeatModeler  | 2.0.6    | <https://github.com/Dfam-consortium/RepeatModeler>
 | 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>
 | HMMER          | 3.4      | <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>
+| RepeatScout    | 1.0.7    | <https://github.com/Dfam-consortium/RepeatScout>
 | RECON          | 1.08     | <http://www.repeatmasker.org/RepeatModeler/RECON-1.08.tar.gz>
 | cd-hit         | 4.8.1    | <https://github.com/weizhongli/cdhit>
 | genometools    | 1.6.4    | <https://github.com/genometools/genometools>

dfam-tetools.sh

@@ -31,7 +31,7 @@ programs are available, singularity is preferred."
 
 ## Parse command-line arguments ##
 
-container="dfam/tetools:1.89.2"
+container="dfam/tetools:1.90"
 use_docker=0
 use_singularity=0
 use_lib=0

getsrc.sh

@@ -27,7 +27,7 @@ download http://www.repeatmasker.org/rmblast/rmblast-2.14.1+-x64-linux.tar.gz
 download http://www.repeatmasker.org/rmblast/rmblast-2.14.1+-arm64-macosx.tar.gz
 download http://eddylab.org/software/hmmer/hmmer-3.4.tar.gz
 download https://github.com/Benson-Genomics-Lab/TRF/archive/v4.09.1.tar.gz trf-4.09.1.tar.gz
-download http://www.repeatmasker.org/RepeatScout-1.0.6.tar.gz
+download https://github.com/Dfam-consortium/RepeatScout/archive/refs/tags/v1.0.7.tar.gz RepeatScout-1.0.7.tar.gz
 download http://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/v1.6.4.tar.gz gt-1.6.4.tar.gz
@@ -39,7 +39,7 @@ 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-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/Dfam-consortium/RepeatModeler/archive/2.0.6.tar.gz RepeatModeler-2.0.6.tar.gz
 # download https://github.com/zhangrengang/TEsorter/archive/v1.4.6.tar.gz TEsorter-1.4.6.tar.gz
 
 # TODO: /exe/ only includes binaries of the "latest" version at the time of download.

sha256sums.txt

@@ -1,21 +1,21 @@
 26172dba3040d1ae5c73ff0ac6c3be8c8e60cc49fc7379e434cdf9cb1e7415de  cd-hit-v4.8.1-2019-0228.tar.gz
 0c48fba155264db8a9e544689678c9f691fee511b74e0b5d227b827657555235  coseg-0.2.3.tar.gz
 31242db2d262305ebdf52c5c7a93743889bdb0f75253750964a0db9e8aa27711  Dfam-RepeatMasker.lib.gz
-bcc8cbe3c0e3b1eb6861cfed4b8495b2b1e28f922623a6bf57f389b76037538e  faToTwoBit_arm64
-d9897ad14695b701e3818c494b2048aa13d089d9b0a7a8b20170d9f87b67e13f  faToTwoBit_x86
+ceac4e6d63ab90fb8cf5f2b612e15e77fad8d92fd89358919ca1bbca21d0dd2f  faToTwoBit_arm64
+65c2e2ec77b560fc30aa49c316f96eef4aac95043cd8239a5b4ea7d02bde435a  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
 15222b39178f19c116282437190b64c5ba68f62b0f2044b3bbcbda5e02748993  RepeatMasker-4.1.7-p1.tar.gz
-4c005ada7e88ff944116832349580a0dc3db762dc1c91235fa574b32ea9a8452  RepeatModeler-2.0.5.tar.gz
-d1d2c32d7343efae3735bc7769b56bc23dd8009c566b7d04f3c796083a7bdace  RepeatScout-1.0.6.tar.gz
+d247b4af42423497c29e7d0649b1b154b4a9aa6968951d7950446549809c1b03  RepeatModeler-2.0.6.tar.gz
+aec393f87aa03efdceb9b664e43de102ed7d83ed1c2cbac3ac53e8cda96e08f9  RepeatScout-1.0.7.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
-803f1638e933e71aed707e60767a0a35fd1310c9459b438dc03819befe535a08  twoBitInfo_arm64
-7915d9c905bca42f6de00134ea052db898b098e34d001c3ea4ad2a3c528a1cf1  twoBitInfo_x86
-24dc672d0773553165a5444ab8182f19cc2c811ff5ad805107fab5144c678910  twoBitToFa_arm64
-a54b36631a280ba1cb3fb88ce8ebbd520d918468648dfce5569a95ba133bfcce  twoBitToFa_x86
+9f27fa6eeefd6634defb1790d3148efc90d9423278c89a4e987b19a7bf972239  twoBitInfo_arm64
+9c04c1e946791a370eefffa89654502a34864851b0d7c8ceb965fc42738f9878  twoBitInfo_x86
+f0b9df760aa84d06ddcbf33bd847e08f9187db0a7070345bb149943b36baba24  twoBitToFa_arm64
+4c1b31073afbdb810d243f45940389ac3715eb183d91c9cbe6495e5d87935565  twoBitToFa_x86