academic/RepeatMasker: Updated for version 4.1.5.

Signed-off-by: Andrew Clemons <andrew.clemons@gmail.com>

Signed-off-by: Willy Sudiarto Raharjo <willysr@slackbuilds.org>

3 files changed, 17 insertions, 26 deletions

diff --git a/academic/RepeatMasker/README.SLACKWARE b/academic/RepeatMasker/README.SLACKWARE
index dd3313fd62..0e92803b9e 100644
--- a/academic/RepeatMasker/README.SLACKWARE
+++ b/academic/RepeatMasker/README.SLACKWARE
@@ -1,31 +1,22 @@
-After install go fo /opt/RepeatMasker and run the RepeatMasker
-Configuration Program:
+After install go to /opt/RepeatMasker and run the Configuration Program:
 
 # perl ./configure
 
-Paths are as follows:
-
-**PERL PROGRAM**
-/usr/bin/perl
-
-**REPEATMASKER INSTALLATION DIRECTORY**
-/opt/RepeatMasker
-
-**TRF PROGRAM**
-/usr/bin/trf
+* The full path including the name for the TRF program.
+TRF_PRGM: /usr/bin/trf
 
 Add a Search Engine:
 1. CrossMatch: you should obtain this yourself, with the proper
    license, following the instructions here http://www.phrap.org/
 2. RMBlast - NCBI Blast with RepeatMasker extensions: this is
    available from SBo.
-3. WUBlast/ABBlast (required by DupMasker): you should obtain this
+3. HMMER3.1 & DFAM: this is available from SBo.
+4. ABBlast/WUBlast (required by DupMasker): you should obtain this
    yourself, with the proper license, following the instructions here
    https://blast.advbiocomp.com/licensing/
-4. HMMER3.1 & DFAM: this is available from SBo.
 
-**RMBlast (rmblastn) INSTALLATION PATH**
+* RMBlast (rmblastn) INSTALLATION PATH
 /usr/bin
 
-**HMMER INSTALLATION PATH**
+* HMMER INSTALLATION PATH
 /usr/bin
diff --git a/academic/RepeatMasker/RepeatMasker.SlackBuild b/academic/RepeatMasker/RepeatMasker.SlackBuild
index 33c83c436d..5d15586aeb 100644
--- a/academic/RepeatMasker/RepeatMasker.SlackBuild
+++ b/academic/RepeatMasker/RepeatMasker.SlackBuild
@@ -2,7 +2,7 @@
 
 # Slackware build script for RepeatMasker
 
-# Copyright 2018-2021 Petar Petrov slackalaxy@gmail.com
+# Copyright 2018-2023 Petar Petrov slackalaxy@gmail.com
 # All rights reserved.
 #
 # Redistribution and use of this script, with or without modification, is
@@ -25,13 +25,12 @@
 cd $(dirname $0) ; CWD=$(pwd)
 
 PRGNAM=RepeatMasker
-VERSION=${VERSION:-4.1.2_p1}
+VERSION=${VERSION:-4.1.5}
 BUILD=${BUILD:-1}
 TAG=${TAG:-_SBo}
 PKGTYPE=${PKGTYPE:-tgz}
 
 ARCH=noarch
-SRCVER=4.1.2-p1
 
 # If the variable PRINT_PACKAGE_NAME is set, then this script will report what
 # the name of the created package would be, and then exit. This information
@@ -52,7 +51,7 @@ rm -rf $PKG
 mkdir -p $TMP $PKG $OUTPUT
 cd $TMP
 rm -rf $PRGNAM
-tar xvf $CWD/$PRGNAM-$SRCVER.tar.gz
+tar xvf $CWD/$PRGNAM-$VERSION.tar.gz
 cd $PRGNAM
 chown -R root:root .
 find -L . \
@@ -65,6 +64,8 @@ find -L . \
 mkdir -p $PKG/opt/$PRGNAM
 cp -a * $PKG/opt/$PRGNAM
 
+rm $PKG/opt/$PRGNAM/{bluegrad.jpg,HTMLAnnotHeader.html,INSTALL,LICENSE,README.md,ReleaseNotes}
+
 # Make a symlink
 mkdir -p $PKG/usr/bin
 cd $PKG/usr/bin
@@ -74,10 +75,9 @@ cd -
 find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \
   | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true
 
-# Better just copy these and not move them from their original dir
 mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION
 cp -a \
-  bluegrad.jpg daterepeats.help HTMLAnnotHeader.html INSTALL LICENSE README.md repeatmasker.help ReleaseNotes \
+  bluegrad.jpg daterepeats.help HTMLAnnotHeader.html LICENSE README.md repeatmasker.help ReleaseNotes \
   $PKG/usr/doc/$PRGNAM-$VERSION
 cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild
 cat $CWD/README.SLACKWARE > $PKG/usr/doc/$PRGNAM-$VERSION/README.SLACKWARE
diff --git a/academic/RepeatMasker/RepeatMasker.info b/academic/RepeatMasker/RepeatMasker.info
index e36cdaf964..3731dbe0f3 100644
--- a/academic/RepeatMasker/RepeatMasker.info
+++ b/academic/RepeatMasker/RepeatMasker.info
@@ -1,10 +1,10 @@
 PRGNAM="RepeatMasker"
-VERSION="4.1.2_p1"
+VERSION="4.1.5"
 HOMEPAGE="http://www.repeatmasker.org/"
-DOWNLOAD="http://www.repeatmasker.org/RepeatMasker/RepeatMasker-4.1.2-p1.tar.gz"
-MD5SUM="fbab50d0c467a9beca316020efc20ee4"
+DOWNLOAD="http://www.repeatmasker.org/RepeatMasker/RepeatMasker-4.1.5.tar.gz"
+MD5SUM="cc9c7ea4303ef11c3d2ca56af5207609"
 DOWNLOAD_x86_64=""
 MD5SUM_x86_64=""
-REQUIRES="perl-Text-Soundex trfind HMMER ncbi-rmblastn"
+REQUIRES="python3-h5py perl-Text-Soundex trfind HMMER ncbi-rmblastn"
 MAINTAINER="Petar Petrov"
 EMAIL="slackalaxy@gmail.com"