From 25b5e0f23027f4b9bb01e66d742aa4ca3a9ca2e5 Mon Sep 17 00:00:00 2001 From: Petar Petrov Date: Fri, 27 Mar 2015 07:57:59 +0700 Subject: academic/fastqc: Added (quality control tool). Signed-off-by: Willy Sudiarto Raharjo --- academic/fastqc/README | 17 ++++++++ academic/fastqc/doinst.sh | 3 ++ academic/fastqc/fastqc.SlackBuild | 84 ++++++++++++++++++++++++++++++++++++++ academic/fastqc/fastqc.desktop | 8 ++++ academic/fastqc/fastqc.info | 10 +++++ academic/fastqc/fastqc.png | Bin 0 -> 1197 bytes academic/fastqc/slack-desc | 19 +++++++++ 7 files changed, 141 insertions(+) create mode 100644 academic/fastqc/README create mode 100644 academic/fastqc/doinst.sh create mode 100644 academic/fastqc/fastqc.SlackBuild create mode 100644 academic/fastqc/fastqc.desktop create mode 100644 academic/fastqc/fastqc.info create mode 100644 academic/fastqc/fastqc.png create mode 100644 academic/fastqc/slack-desc (limited to 'academic/fastqc') diff --git a/academic/fastqc/README b/academic/fastqc/README new file mode 100644 index 0000000000..ef3be171ac --- /dev/null +++ b/academic/fastqc/README @@ -0,0 +1,17 @@ +FastQC: A quality control tool for high throughput sequence data + +FastQC aims to provide a simple way to do some quality control checks +on raw sequence data coming from high throughput sequencing pipelines. +It provides a modular set of analyses which you can use to give a +quick impression of whether your data has any problems of which you +should be aware before doing any further analysis. + +The main functions of FastQC are + +- Import of data from BAM, SAM or FastQ files (any variant) +- Providing a quick overview to tell you in which areas there may be + problems +- Summary graphs and tables to quickly assess your data +- Export of results to an HTML based permanent report +- Offline operation to allow automated generation of reports without + running the interactive application diff --git a/academic/fastqc/doinst.sh b/academic/fastqc/doinst.sh new file mode 100644 index 0000000000..5fb28930db --- /dev/null +++ b/academic/fastqc/doinst.sh @@ -0,0 +1,3 @@ +if [ -x /usr/bin/update-desktop-database ]; then + /usr/bin/update-desktop-database -q usr/share/applications >/dev/null 2>&1 +fi diff --git a/academic/fastqc/fastqc.SlackBuild b/academic/fastqc/fastqc.SlackBuild new file mode 100644 index 0000000000..b489ef39ec --- /dev/null +++ b/academic/fastqc/fastqc.SlackBuild @@ -0,0 +1,84 @@ +#!/bin/sh + +# Slackware build script for fastqc + +# Copyright 2015 Petar Petrov petar.petrov@student.oulu.fi +# 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=fastqc +SRCNAM=FastQC +VERSION=${VERSION:-0.11.2} +SRCVER=${SRCVER:-v0.11.2} + +BUILD=${BUILD:-1} +TAG=${TAG:-_SBo} + +ARCH=noarch + +# Jar files names and versions +JBZIP=jbzip2-0.9.jar +SAM=sam-1.103.jar + +CWD=$(pwd) +TMP=${TMP:-/tmp/SBo} +PKG=$TMP/package-$PRGNAM +OUTPUT=${OUTPUT:-/tmp} + +set -e + +rm -rf $PKG +mkdir -p $TMP $PKG $OUTPUT +cd $TMP +rm -rf $SRCNAM +unzip $CWD/${PRGNAM}_${SRCVER}.zip +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 {} \; + +install -D -m755 $PRGNAM $PKG/usr/share/java/$PRGNAM/$PRGNAM +cp -a Configuration net org Templates uk $JBZIP $SAM $PKG/usr/share/java/$PRGNAM + +mkdir -p $PKG/usr/bin +cd $PKG/usr/bin +ln -s ../share/java/$PRGNAM/$PRGNAM +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 + +mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION +cp -a Help *.txt $PKG/usr/doc/$PRGNAM-$VERSION +cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild + +# Menu item and icon +mkdir -p $PKG/usr/share/{applications,pixmaps} +cp $CWD/$PRGNAM.desktop $PKG/usr/share/applications +cp $CWD/$PRGNAM.png $PKG/usr/share/pixmaps + +mkdir -p $PKG/install +cat $CWD/slack-desc > $PKG/install/slack-desc +cat $CWD/doinst.sh > $PKG/install/doinst.sh + +cd $PKG +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.${PKGTYPE:-tgz} diff --git a/academic/fastqc/fastqc.desktop b/academic/fastqc/fastqc.desktop new file mode 100644 index 0000000000..25d61cb7ef --- /dev/null +++ b/academic/fastqc/fastqc.desktop @@ -0,0 +1,8 @@ +[Desktop Entry] +Name=FastQC +Comment=A quality control tool for high throughput sequence data +Exec=fastqc +Icon=fastqc +StartupNotify=false +Type=Application +Categories=Education; diff --git a/academic/fastqc/fastqc.info b/academic/fastqc/fastqc.info new file mode 100644 index 0000000000..d9c10eca67 --- /dev/null +++ b/academic/fastqc/fastqc.info @@ -0,0 +1,10 @@ +PRGNAM="fastqc" +VERSION="0.11.2" +HOMEPAGE="http://www.bioinformatics.babraham.ac.uk/projects/fastqc/" +DOWNLOAD="http://www.bioinformatics.babraham.ac.uk/projects/fastqc/fastqc_v0.11.2.zip" +MD5SUM="8686e180a2d7c818821eb7db194d9488" +DOWNLOAD_x86_64="" +MD5SUM_x86_64="" +REQUIRES="jdk" +MAINTAINER="Petar Petrov" +EMAIL="petar.petrov@student.oulu.fi" diff --git a/academic/fastqc/fastqc.png b/academic/fastqc/fastqc.png new file mode 100644 index 0000000000..348c93b95d Binary files /dev/null and b/academic/fastqc/fastqc.png differ diff --git a/academic/fastqc/slack-desc b/academic/fastqc/slack-desc new file mode 100644 index 0000000000..ee41491c01 --- /dev/null +++ b/academic/fastqc/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------------------------------------------------------| +fastqc: fastqc (A quality control tool for high throughput sequence data) +fastqc: +fastqc: FastQC aims to provide a simple way to do some quality control +fastqc: checks on raw sequence data coming from high throughput +fastqc: sequencing pipelines. It provides a modular set of analyses +fastqc: which you can use to give a quick impression of whether your +fastqc: data has any problems of which you should be aware before +fastqc: doing any further analysis. +fastqc: +fastqc: Home: http://www.bioinformatics.babraham.ac.uk/projects/fastqc/ +fastqc: -- cgit v1.2.3