From 3e67292656c9c8244936597589a841f22d2ac84f Mon Sep 17 00:00:00 2001 From: Petar Petrov Date: Sun, 5 Jan 2020 03:52:05 -0600 Subject: academic/meme-db-tgene: Added (MEME Suite T-gene databases) Signed-off-by: Robby Workman --- academic/meme-db-tgene/README | 26 ++++++++++ academic/meme-db-tgene/meme-db-tgene.SlackBuild | 65 +++++++++++++++++++++++++ academic/meme-db-tgene/meme-db-tgene.info | 10 ++++ academic/meme-db-tgene/slack-desc | 19 ++++++++ 4 files changed, 120 insertions(+) create mode 100644 academic/meme-db-tgene/README create mode 100644 academic/meme-db-tgene/meme-db-tgene.SlackBuild create mode 100644 academic/meme-db-tgene/meme-db-tgene.info create mode 100644 academic/meme-db-tgene/slack-desc (limited to 'academic') diff --git a/academic/meme-db-tgene/README b/academic/meme-db-tgene/README new file mode 100644 index 0000000000..57026d4c12 --- /dev/null +++ b/academic/meme-db-tgene/README @@ -0,0 +1,26 @@ +T-Gene Databases (updated 12 Oct 2019) to be used with MEME Suite: + +Genome + Histone/Expression Data +Human hg19 (ENCODE Tissue Panel) +Human hg19 (Epigenomic Roadmap Tissue Panel) +Mouse mm9 (ENCODE Tissue Panel) + +Genomes Only +Arabidopsis thaliana TAIR10 (Ensembl) +Caenorhabditis elegans WBcel235 (Ensembl) +Caenorhabditis elegans ce11 (UCSC) +Danio rerio GRCz11 (Ensembl) +Danio rerio danRer11 (UCSC) +Drosophila melanogaster BDGP6 (Ensembl) +Drosophila melanogaster dm6 (UCSC) +Homo sapiens GRCh38 (Ensembl) +Homo sapiens hg38 (UCSC) +Mus musculus GRCm38 (Ensembl) +Mus musculus mm10 (UCSC) +Rattus norvegicus Rnor_6 (Ensembl) +Rattus norvegicus rn6 (UCSC) +Saccharomyces cerevisiae R64-1-1 (Ensembl) +Saccharomyces cerevisiae sacCer3 (UCSC) + +Note!!! +The unarchived size of this is ~2.6 GB diff --git a/academic/meme-db-tgene/meme-db-tgene.SlackBuild b/academic/meme-db-tgene/meme-db-tgene.SlackBuild new file mode 100644 index 0000000000..95e75e5a5c --- /dev/null +++ b/academic/meme-db-tgene/meme-db-tgene.SlackBuild @@ -0,0 +1,65 @@ +#!/bin/sh + +# Slackware build script for meme-db-tgene + +# Copyright 2020 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. + +PRGNAM=meme-db-tgene +VERSION=${VERSION:-1.0} +BUILD=${BUILD:-1} +TAG=${TAG:-_SBo} + +SRCNAM=tgene_databases + +ARCH=noarch + +CWD=$(pwd) +TMP=${TMP:-/tmp/SBo} +PKG=$TMP/package-$PRGNAM +OUTPUT=${OUTPUT:-/tmp} + +set -e + +rm -rf $PKG +mkdir -p $TMP $PKG $OUTPUT +cd $PKG + +# Extract directly in the $PKG folder +mkdir -p var/lib/meme-suite +cd var/lib/meme-suite +tar xvf $CWD/${SRCNAM}.${VERSION}.tgz +cd $SRCNAM + +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 {} \; + +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:-tgz} diff --git a/academic/meme-db-tgene/meme-db-tgene.info b/academic/meme-db-tgene/meme-db-tgene.info new file mode 100644 index 0000000000..6c90f7f5d3 --- /dev/null +++ b/academic/meme-db-tgene/meme-db-tgene.info @@ -0,0 +1,10 @@ +PRGNAM="meme-db-tgene" +VERSION="1.0" +HOMEPAGE="http://meme-suite.org/db/tgene" +DOWNLOAD="http://meme-suite.org/meme-software/Databases/tgene/tgene_databases.1.0.tgz" +MD5SUM="8a2e467f979a4721e4fb2233bf2b0a04" +DOWNLOAD_x86_64="" +MD5SUM_x86_64="" +REQUIRES="" +MAINTAINER="Petar Petrov" +EMAIL="slackalaxy@gmail.com" diff --git a/academic/meme-db-tgene/slack-desc b/academic/meme-db-tgene/slack-desc new file mode 100644 index 0000000000..c1a6e06666 --- /dev/null +++ b/academic/meme-db-tgene/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------------------------------------------------------| +meme-db-tgene: meme-db-tgene (MEME Suite T-gene databases) +meme-db-tgene: +meme-db-tgene: T-Gene Databases to be used with MEME Suite: +meme-db-tgene: +meme-db-tgene: Genome + Histone/Expression Data +meme-db-tgene: Genomes Only +meme-db-tgene: +meme-db-tgene: +meme-db-tgene: +meme-db-tgene: +meme-db-tgene: -- cgit v1.2.3