academic/ncbi-edirect: Added (Entrez Direct cli utilities).

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

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

4 files changed, 159 insertions, 0 deletions

diff --git a/academic/ncbi-edirect/README b/academic/ncbi-edirect/README
new file mode 100644
index 000000000000..f318903e06ee
--- /dev/null
+++ b/academic/ncbi-edirect/README
@@ -0,0 +1,8 @@
+Entrez Direct: E-utilities on the Unix Command Line
+
+Entrez Direct (EDirect) provides access to the NCBI's suite of inter-
+connected databases (publication, sequence, structure, gene, variation,
+expression, etc.) from a Unix terminal window. Search terms are entered
+as command-line arguments. Individual operations are connected with Unix
+pipes to construct multi-step queries. Selected records can then be
+retrieved in a variety of formats.
diff --git a/academic/ncbi-edirect/ncbi-edirect.SlackBuild b/academic/ncbi-edirect/ncbi-edirect.SlackBuild
new file mode 100644
index 000000000000..aa3a827f04d9
--- /dev/null
+++ b/academic/ncbi-edirect/ncbi-edirect.SlackBuild
@@ -0,0 +1,114 @@
+#!/bin/bash
+
+# Slackware build script for ncbi-edirect
+
+# Copyright 2023 Petar Petrov, slackalaxy@gmail.com
+# All rights reserved.
+#
+# Redistribution and use of this script, with or without modification, is
+# permitted provided that the following conditions are met:
+#
+# 1. Redistributions of this script must retain the above copyright
+#    notice, this list of conditions and the following disclaimer.
+#
+#  THIS SOFTWARE IS PROVIDED BY THE AUTHOR "AS IS" AND ANY EXPRESS OR IMPLIED
+#  WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF
+#  MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED.  IN NO
+#  EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+#  SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+#  PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+#  OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+#  WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+#  OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+#  ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+
+cd $(dirname $0) ; CWD=$(pwd)
+
+PRGNAM=ncbi-edirect
+VERSION=${VERSION:-20.4.20230915}
+BUILD=${BUILD:-1}
+TAG=${TAG:-_SBo}
+PKGTYPE=${PKGTYPE:-tgz}
+
+MANPG=ncbi-entrez-direct_19.0.20230216+dfsg-2.debian.tar.xz
+
+if [ -z "$ARCH" ]; then
+  case "$( uname -m )" in
+    i?86) ARCH=i586 ;;
+    arm*) ARCH=arm ;;
+       *) ARCH=$( uname -m ) ;;
+  esac
+fi
+
+if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then
+  echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE"
+  exit 0
+fi
+
+if [ "$ARCH" != "x86_64" ]; then
+  printf "\n$ARCH is not supported... \n"
+  exit 1
+fi
+
+TMP=${TMP:-/tmp/SBo}
+PKG=$TMP/package-$PRGNAM
+OUTPUT=${OUTPUT:-/tmp}
+
+set -e
+
+rm -rf $PKG
+mkdir -p $TMP $PKG $OUTPUT
+cd $TMP
+rm -rf $PRGNAM-$VERSION
+mkdir $PRGNAM-$VERSION
+cd $PRGNAM-$VERSION
+
+tar xvf $CWD/edirect-$VERSION.tar.gz
+cd edirect
+tar xvf $CWD/$MANPG
+chown -R root:root .
+find -L . \
+ \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \
+  -o -perm 511 \) -exec chmod 755 {} \; -o \
+ \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \
+  -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \;
+
+# Move these to their proper place
+mkdir -p $PKG/usr/share/$PRGNAM
+mv ./{cmd,eutils} $PKG/usr/share/$PRGNAM
+
+mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION
+mv ./{help,readme.pdf,README} $PKG/usr/doc/$PRGNAM-$VERSION
+
+# remove these
+rm -rf ./{CA.pm,cacert.pem,Mozilla-CA.tar.gz}
+
+# include the binaries
+mkdir -p $PKG/usr/bin
+gunzip -c $CWD/rchive.Linux.gz > $PKG/usr/bin/rchive.Linux
+gunzip -c $CWD/transmute.Linux.gz > $PKG/usr/bin/transmute.Linux
+gunzip -c $CWD/xtract.Linux.gz > $PKG/usr/bin/xtract.Linux
+chmod 755 $PKG/usr/bin/*
+
+# thanks Debian for the man pages
+mkdir -p $PKG/usr/man/man1
+cp -a debian/man/* $PKG/usr/man/man1
+rm -rf debian
+
+# move what's left
+cp -a * $PKG/usr/bin
+
+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
+
+find $PKG/usr/man -type f -exec gzip -9 {} \;
+for i in $( find $PKG/usr/man -type l ) ; do ln -s $( readlink $i ).gz $i.gz ; rm $i ; done
+
+mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION
+cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild
+
+mkdir -p $PKG/install
+cat $CWD/slack-desc > $PKG/install/slack-desc
+
+cd $PKG
+/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE
diff --git a/academic/ncbi-edirect/ncbi-edirect.info b/academic/ncbi-edirect/ncbi-edirect.info
new file mode 100644
index 000000000000..01a96d1fa3ea
--- /dev/null
+++ b/academic/ncbi-edirect/ncbi-edirect.info
@@ -0,0 +1,18 @@
+PRGNAM="ncbi-edirect"
+VERSION="20.4.20230915"
+HOMEPAGE="https://www.ncbi.nlm.nih.gov/books/NBK179288/"
+DOWNLOAD="UNSUPPORTED"
+MD5SUM=""
+DOWNLOAD_x86_64="https://ftp.ncbi.nlm.nih.gov/entrez/entrezdirect/versions/20.4.20230915/edirect-20.4.20230915.tar.gz \
+https://ftp.ncbi.nlm.nih.gov/entrez/entrezdirect/versions/20.4.20230915/rchive.Linux.gz \
+https://ftp.ncbi.nlm.nih.gov/entrez/entrezdirect/versions/20.4.20230915/transmute.Linux.gz \
+https://ftp.ncbi.nlm.nih.gov/entrez/entrezdirect/versions/20.4.20230915/xtract.Linux.gz \
+http://deb.debian.org/debian/pool/main/n/ncbi-entrez-direct/ncbi-entrez-direct_19.0.20230216+dfsg-2.debian.tar.xz"
+MD5SUM_x86_64="8bf8634cc90c5b7bc2af3c03dcccdc7b \
+397531a92c8ed47a51c5d047845e9f62 \
+d6a0721a4b4f558e1a42ac4fe71da728 \
+9a5b5db65708b92eff88883e3dae6747 \
+f640a8d59b75655b411c984c984efef0"
+REQUIRES=""
+MAINTAINER="Petar Petrov"
+EMAIL="slackalaxy@gmail.com"
diff --git a/academic/ncbi-edirect/slack-desc b/academic/ncbi-edirect/slack-desc
new file mode 100644
index 000000000000..8cbe8e8cd5ef
--- /dev/null
+++ b/academic/ncbi-edirect/slack-desc
@@ -0,0 +1,19 @@
+# HOW TO EDIT THIS FILE:
+# The "handy ruler" below makes it easier to edit a package description.
+# Line up the first '|' above the ':' following the base package name, and
+# the '|' on the right side marks the last column you can put a character in.
+# You must make exactly 11 lines for the formatting to be correct.  It's also
+# customary to leave one space after the ':' except on otherwise blank lines.
+
+            |-----handy-ruler------------------------------------------------------|
+ncbi-edirect: ncbi-edirect (E-utilities on the Unix Command Line)
+ncbi-edirect:
+ncbi-edirect: Entrez Direct (EDirect) provides access to the NCBI's suite of
+ncbi-edirect: interconnected databases from a Unix terminal window.
+ncbi-edirect:
+ncbi-edirect: https://www.ncbi.nlm.nih.gov/books/NBK179288/
+ncbi-edirect:
+ncbi-edirect:
+ncbi-edirect:
+ncbi-edirect:
+ncbi-edirect: