Update RepeatMasker recipe (bioconda#50757)

* Update RepeatMasker recipe * edit build.sh * edit build.sh * edit build.sh
mencian · Sep 17, 2024 · eb79e19 · eb79e19
1 parent 37e6f2b
commit eb79e19
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Showing 3 changed files with 16 additions and 8 deletions.
diff --git a/recipes/repeatmasker/build.sh b/recipes/repeatmasker/build.sh
@@ -38,5 +38,13 @@ for name in ${RM_DIR}/util/* ; do
 done
 
 # Fix perl shebang
+sed -i.bak '1 s|^.*$|#!/usr/bin/env perl|g' ${RM_DIR}/RepeatMasker
+sed -i.bak '1 s|^.*$|#!/usr/bin/env perl|g' ${RM_DIR}/DupMasker
+sed -i.bak '1 s|^.*$|#!/usr/bin/env perl|g' ${RM_DIR}/ProcessRepeats
+sed -i.bak '1 s|^.*$|#!/usr/bin/env perl|g' ${RM_DIR}/RepeatProteinMask
 sed -i.bak '1 s|^.*$|#!/usr/bin/env perl|g' ${RM_DIR}/util/*.pl
+sed -i.bak '1 s|^.*$|#!/usr/bin/env perl|g' ${RM_DIR}/*.pm
+sed -i.bak '1 s|^.*$|#!/usr/bin/env perl|g' ${RM_DIR}/*.pl
+
 rm -rf ${RM_DIR}/util/*.bak
+rm -rf ${RM_DIR}/*.bak
diff --git a/recipes/repeatmasker/meta.yaml b/recipes/repeatmasker/meta.yaml
@@ -11,7 +11,7 @@ source:
   sha256: {{ sha256 }}
 
 build:
-  number: 0
+  number: 1
   noarch: generic
   run_exports:
     - {{ pin_subpackage('repeatmasker', max_pin='x') }}

diff --git a/recipes/repeatmasker/post-link.sh b/recipes/repeatmasker/post-link.sh
@@ -4,14 +4,14 @@ if [[ -f /.dockerenv ]]; then
     cat >> "$PREFIX/.messages.txt" <<EOF
 To install the databases needed by RepeatMasker, execute:
 
-wget -O Dfam_curatedonly.h5.gz https://www.dfam.org/releases/Dfam_3.7/families/Dfam_curatedonly.h5.gz
-gunzip -c Dfam_curatedonly.h5.gz > ${PREFIX}/share/RepeatMasker/Libraries/Dfam.h5
-rm -rf Dfam_curatedonly.h5.gz
+wget -O Dfam-RepeatMasker.lib.gz https://www.dfam.org/releases/Dfam_3.8/families/Dfam-RepeatMasker.lib.gz
+gunzip -c Dfam-RepeatMasker.lib.gz > ${PREFIX}/share/RepeatMasker/Libraries/RepeatMasker.lib
+rm -rf Dfam-RepeatMasker.lib.gz
 
 EOF
 else
-    echo "Downloading Dfam_curatedonly.h5.gz from www.dfam.org"
-    wget -O Dfam_curatedonly.h5.gz https://www.dfam.org/releases/Dfam_3.7/families/Dfam_curatedonly.h5.gz
-    gunzip -c Dfam_curatedonly.h5.gz > ${PREFIX}/share/RepeatMasker/Libraries/Dfam.h5
-    rm -rf Dfam_curatedonly.h5.gz
+    echo "Dfam-RepeatMasker.lib.gz from www.dfam.org"
+    wget -O Dfam-RepeatMasker.lib.gz https://www.dfam.org/releases/Dfam_3.8/families/Dfam-RepeatMasker.lib.gz
+    gunzip -c Dfam-RepeatMasker.lib.gz > ${PREFIX}/share/RepeatMasker/Libraries/RepeatMasker.lib
+    rm -rf Dfam-RepeatMasker.lib.gz
 fi