code stringlengths 1 1.96M | language stringclasses 1
value |
|---|---|
#!/bin/sh
#
# Copyright (c) 2002-2006
# The Thunar development team. All rights reserved.
#
# Written for Thunar by Benedikt Meurer <benny@xfce.org>.
#
(type xdt-autogen) >/dev/null 2>&1 || {
cat >&2 <<EOF
autogen.sh: You don't seem to have the Xfce development tools installed on
your system, whi... | Shell |
#!/bin/sh
prefix="@prefix@"
exec_prefix="@exec_prefix@"
exec_prefix_set=no
usage="\
Usage: libmpq-config [--prefix[=DIR]] [--exec-prefix[=DIR]] [--version] [--libs] [--cflags]"
if test "$#" -eq "0"; then
echo "${usage}" 1>&2
exit 1
fi
while test "$#" -gt "0"; do
case "$1" in
-*=*) optarg=`echo "$1" ... | Shell |
#!/bin/sh
#
echo "Generating build information using aclocal, autoheader, automake and autoconf"
echo "This may take a while ..."
# Touch the timestamps on all the files since CVS messes them up
directory=`dirname $0`
touch $directory/configure.ac
# Regenerate configuration files
libtoolize --copy
aclocal
autoheader
... | Shell |
#!/bin/bash
# Massive Network Game Object Server
# Monitoring Script
pid=`ps ax | awk '($5 ~ /mangos-worldd/) { print $1 }'`
cpu=`top -b -n 1 -p $pid | awk '($12 ~ /mangos-worldd/) { print $9 }'`
#echo $pid
#echo $cpu
intcpu=${cpu%.*}
#echo $intcpu
if [ "$intcpu" -gt "95" ]
then
kill -9 $pid
echo "Killed MaNGOS for ... | Shell |
#!/bin/bash
# Trinity Server
# autorestart Script
while :
do
echo "TrinityCore daemon restarted"
echo `date` >> crash.log &
./mangosd | tail -n 20 >> crash.log
echo " " >> crash.log &
pid=`ps ax | awk '($5 ~ /trinitycore/) { print $1 }'`
wait $pid
echo `date` ", TrinityCore daemon crashed and restarted.... | Shell |
#! /bin/bash
OREGON_DIR='/opt/oregon/';
RETVAL=0;
start(){
screen -AmdS oregon_restarter ${OREGON_DIR}restarter
}
stop(){
screen -dr oregon_restarter -X "quit"
}
start-realm(){
screen -AmdS oregon_realm ${OREGON_DIR}bin/oregon-realm -c ${OREGON_DIR}etc/oregonrealm.conf
}
stop-realm(){
screen -dr oregon_realm -X... | Shell |
chmod +x oregon restarter
cp oregon /etc/init.d/
cp restarter /opt/oregon/
| Shell |
#! /bin/bash
while true
do
PID1=$(pidof oregon-core)
if (( PID1 < 1 ))
then
/etc/init.d/oregon start-core
fi
PID2=$(pidof oregon-realm)
if (( PID2 < 1 ))
then
/etc/init.d/oregon start-realm
fi
sleep 10
done
| Shell |
rm -rf assembled
mkdir assembled
rm -rf target
mvn package -e -P generic
cp target/jbrowser-1.9-jar-with-dependencies.jar assembled/jbrowser-1.9-generic.jar
rm -rf target
mvn package -e -P linux
cp target/jbrowser-1.9-jar-with-dependencies.jar assembled/jbrowser-1.9-linux.jar
rm -rf target
mvn package -e -P solaris
... | Shell |
#!/bin/sh
# START-COMMIT HOOK
#
# The start-commit hook is invoked before a Subversion txn is created
# in the process of doing a commit. Subversion runs this hook
# by invoking a program (script, executable, binary, etc.) named
# 'start-commit' (for which this file is a template)
# with the following ordered... | Shell |
#!/bin/sh
# PRE-COMMIT HOOK
#
# The pre-commit hook is invoked before a Subversion txn is
# committed. Subversion runs this hook by invoking a program
# (script, executable, binary, etc.) named 'pre-commit' (for which
# this file is a template), with the following ordered arguments:
#
# [1] REPOS-PATH (t... | Shell |
#!/bin/sh
# PRE-LOCK HOOK
#
# The pre-lock hook is invoked before an exclusive lock is
# created. Subversion runs this hook by invoking a program
# (script, executable, binary, etc.) named 'pre-lock' (for which
# this file is a template), with the following ordered arguments:
#
# [1] REPOS-PATH (the pat... | Shell |
#!/bin/sh
# POST-COMMIT HOOK
#
# The post-commit hook is invoked after a commit. Subversion runs
# this hook by invoking a program (script, executable, binary, etc.)
# named 'post-commit' (for which this file is a template) with the
# following ordered arguments:
#
# [1] REPOS-PATH (the path to this rep... | Shell |
#!/bin/sh
# PRE-COMMIT HOOK
#
# The pre-commit hook is invoked before a Subversion txn is
# committed. Subversion runs this hook by invoking a program
# (script, executable, binary, etc.) named 'pre-commit' (for which
# this file is a template), with the following ordered arguments:
#
# [1] REPOS-PATH (t... | Shell |
#!/bin/sh
# PRE-REVPROP-CHANGE HOOK
#
# The pre-revprop-change hook is invoked before a revision property
# is added, modified or deleted. Subversion runs this hook by invoking
# a program (script, executable, binary, etc.) named 'pre-revprop-change'
# (for which this file is a template), with the following or... | Shell |
#!/bin/sh
# PRE-LOCK HOOK
#
# The pre-lock hook is invoked before an exclusive lock is
# created. Subversion runs this hook by invoking a program
# (script, executable, binary, etc.) named 'pre-lock' (for which
# this file is a template), with the following ordered arguments:
#
# [1] REPOS-PATH (the pat... | Shell |
#!/bin/sh
# POST-REVPROP-CHANGE HOOK
#
# The post-revprop-change hook is invoked after a revision property
# has been added, modified or deleted. Subversion runs this hook by
# invoking a program (script, executable, binary, etc.) named
# 'post-revprop-change' (for which this file is a template), with the
# f... | Shell |
#!/bin/sh
# POST-LOCK HOOK
#
# The post-lock hook is run after a path is locked. Subversion runs
# this hook by invoking a program (script, executable, binary, etc.)
# named 'post-lock' (for which this file is a template) with the
# following ordered arguments:
#
# [1] REPOS-PATH (the path to this repos... | Shell |
#!/bin/sh
# PRE-UNLOCK HOOK
#
# The pre-unlock hook is invoked before an exclusive lock is
# destroyed. Subversion runs this hook by invoking a program
# (script, executable, binary, etc.) named 'pre-unlock' (for which
# this file is a template), with the following ordered arguments:
#
# [1] REPOS-PATH ... | Shell |
#!/bin/sh
# START-COMMIT HOOK
#
# The start-commit hook is invoked before a Subversion txn is created
# in the process of doing a commit. Subversion runs this hook
# by invoking a program (script, executable, binary, etc.) named
# 'start-commit' (for which this file is a template)
# with the following ordered... | Shell |
#!/bin/sh
# POST-COMMIT HOOK
#
# The post-commit hook is invoked after a commit. Subversion runs
# this hook by invoking a program (script, executable, binary, etc.)
# named 'post-commit' (for which this file is a template) with the
# following ordered arguments:
#
# [1] REPOS-PATH (the path to this rep... | Shell |
#!/bin/sh
# POST-UNLOCK HOOK
#
# The post-unlock hook runs after a path is unlocked. Subversion runs
# this hook by invoking a program (script, executable, binary, etc.)
# named 'post-unlock' (for which this file is a template) with the
# following ordered arguments:
#
# [1] REPOS-PATH (the path to this... | Shell |
#!/bin/sh
# POST-UNLOCK HOOK
#
# The post-unlock hook runs after a path is unlocked. Subversion runs
# this hook by invoking a program (script, executable, binary, etc.)
# named 'post-unlock' (for which this file is a template) with the
# following ordered arguments:
#
# [1] REPOS-PATH (the path to this... | Shell |
#!/bin/sh
# PRE-REVPROP-CHANGE HOOK
#
# The pre-revprop-change hook is invoked before a revision property
# is added, modified or deleted. Subversion runs this hook by invoking
# a program (script, executable, binary, etc.) named 'pre-revprop-change'
# (for which this file is a template), with the following or... | Shell |
#!/bin/sh
# POST-LOCK HOOK
#
# The post-lock hook is run after a path is locked. Subversion runs
# this hook by invoking a program (script, executable, binary, etc.)
# named 'post-lock' (for which this file is a template) with the
# following ordered arguments:
#
# [1] REPOS-PATH (the path to this repos... | Shell |
#!/bin/sh
# POST-REVPROP-CHANGE HOOK
#
# The post-revprop-change hook is invoked after a revision property
# has been added, modified or deleted. Subversion runs this hook by
# invoking a program (script, executable, binary, etc.) named
# 'post-revprop-change' (for which this file is a template), with the
# f... | Shell |
#!/bin/sh
# PRE-UNLOCK HOOK
#
# The pre-unlock hook is invoked before an exclusive lock is
# destroyed. Subversion runs this hook by invoking a program
# (script, executable, binary, etc.) named 'pre-unlock' (for which
# this file is a template), with the following ordered arguments:
#
# [1] REPOS-PATH ... | Shell |
#!/bin/sh
#
# San Angeles Observation OpenGL ES version example
#
# This shell script builds the demo application
# with executable name "SanOGLES".
#
# Before running it, make sure that either libGLES_CM.so
# or libGLES_CL.so is available in the library path.
# Alternatively you can copy one of them to the same
# dire... | Shell |
#!/bin/ksh
# launcher script for jsdoc
# Author: Avi Deitcher
#
# This program is released under the MIT License as follows:
# Copyright (c) 2008-2009 Atomic Inc <avi@jsorm.com>
#
#Permission is hereby granted, free of charge, to any person
#obtaining a copy of this software and associated documentation
#files (the "... | Shell |
#! /bin/sh
# mkinstalldirs --- make directory hierarchy
scriptversion=2009-04-28.21; # UTC
# Original author: Noah Friedman <friedman@prep.ai.mit.edu>
# Created: 1993-05-16
# Public domain.
#
# This file is maintained in Automake, please report
# bugs to <bug-automake@gnu.org> or send patches to
# <automake-patches@g... | Shell |
#!/bin/sh
# Run this to generate all the initial makefiles, etc.
srcdir=`dirname $0`
test -z "$srcdir" && srcdir=.
DIE=0
if [ -n "$GNOME2_DIR" ]; then
ACLOCAL_FLAGS="-I $GNOME2_DIR/share/aclocal $ACLOCAL_FLAGS"
LD_LIBRARY_PATH="$GNOME2_DIR/lib:$LD_LIBRARY_PATH"
PATH="$GNOME2_DIR/bin:$PATH"
export PATH
export LD... | Shell |
#!/bin/bash
curl -O https://tesseract-ocr.googlecode.com/files/tesseract-ocr-3.02.02.tar.gz
curl -O http://leptonica.googlecode.com/files/leptonica-1.69.tar.gz
tar -zxvf tesseract-ocr-3.02.02.tar.gz
tar -zxvf leptonica-1.69.tar.gz
rm -f tesseract-ocr-3.02.02.tar.gz
rm -f leptonica-1.69.tar.gz
mv tesseract-ocr jni/com_g... | Shell |
#!/bin/bash
curl -O http://tesseract-ocr.googlecode.com/files/tesseract-ocr-3.02.eng.tar.gz
tar -zxvf tesseract-ocr-3.02.eng.tar.gz
rm -f tesseract-ocr-3.02.eng.tar.gz
mkdir data
mv tesseract-ocr data/tesseract
adb push data/ /sdcard/
adb shell sync
| Shell |
#! /bin/sh
# depcomp - compile a program generating dependencies as side-effects
scriptversion=2007-03-29.01
# Copyright (C) 1999, 2000, 2003, 2004, 2005, 2006, 2007 Free Software
# Foundation, Inc.
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public ... | Shell |
#! /bin/sh
# libtool - Provide generalized library-building support services.
# Generated automatically by config.status (xfmpc) 0.1.0
# Libtool was configured on host saturn:
# NOTE: Changes made to this file will be lost: look at ltmain.sh.
#
# Copyright (C) 1996, 1997, 1998, 1999, 2000, 2001, 2003, 2004, 2005,
# ... | Shell |
# Generated from ltmain.m4sh.
# ltmain.sh (GNU libtool) 2.2.6
# Written by Gordon Matzigkeit <gord@gnu.ai.mit.edu>, 1996
# Copyright (C) 1996, 1997, 1998, 1999, 2000, 2001, 2003, 2004, 2005, 2006, 2007 2008 Free Software Foundation, Inc.
# This is free software; see the source for copying conditions. There is NO
# w... | Shell |
#!/bin/sh
# install - install a program, script, or datafile
scriptversion=2006-12-25.00
# This originates from X11R5 (mit/util/scripts/install.sh), which was
# later released in X11R6 (xc/config/util/install.sh) with the
# following copyright and license.
#
# Copyright (C) 1994 X Consortium
#
# Permission is hereby ... | Shell |
#! /bin/sh
# mkinstalldirs --- make directory hierarchy
scriptversion=2006-05-11.19
# Original author: Noah Friedman <friedman@prep.ai.mit.edu>
# Created: 1993-05-16
# Public domain.
#
# This file is maintained in Automake, please report
# bugs to <bug-automake@gnu.org> or send patches to
# <automake-patches@gnu.org>... | Shell |
#! /bin/sh
# Wrapper for compilers which do not understand `-c -o'.
scriptversion=2005-05-14.22
# Copyright (C) 1999, 2000, 2003, 2004, 2005 Free Software Foundation, Inc.
# Written by Tom Tromey <tromey@cygnus.com>.
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the ... | Shell |
#! /bin/sh
# depcomp - compile a program generating dependencies as side-effects
scriptversion=2007-03-29.01
# Copyright (C) 1999, 2000, 2003, 2004, 2005, 2006, 2007 Free Software
# Foundation, Inc.
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public ... | Shell |
#! /bin/sh
# libtool - Provide generalized library-building support services.
# Generated automatically by config.status (xfmpc) 0.1.0
# Libtool was configured on host saturn:
# NOTE: Changes made to this file will be lost: look at ltmain.sh.
#
# Copyright (C) 1996, 1997, 1998, 1999, 2000, 2001, 2003, 2004, 2005,
# ... | Shell |
#! /bin/sh
# Common stub for a few missing GNU programs while installing.
scriptversion=2006-05-10.23
# Copyright (C) 1996, 1997, 1999, 2000, 2002, 2003, 2004, 2005, 2006
# Free Software Foundation, Inc.
# Originally by Fran,cois Pinard <pinard@iro.umontreal.ca>, 1996.
# This program is free software; you can redi... | Shell |
#! /bin/sh
# Configuration validation subroutine script.
# Copyright (C) 1992, 1993, 1994, 1995, 1996, 1997, 1998, 1999,
# 2000, 2001, 2002, 2003, 2004, 2005, 2006, 2007, 2008
# Free Software Foundation, Inc.
timestamp='2008-09-08'
# This file is (in principle) common to ALL GNU software.
# The presence of a ma... | Shell |
#! /bin/sh
# Attempt to guess a canonical system name.
# Copyright (C) 1992, 1993, 1994, 1995, 1996, 1997, 1998, 1999,
# 2000, 2001, 2002, 2003, 2004, 2005, 2006, 2007, 2008
# Free Software Foundation, Inc.
timestamp='2008-11-15'
# This file is free software; you can redistribute it and/or modify it
# under the... | Shell |
#!/bin/sh
# install - install a program, script, or datafile
scriptversion=2006-12-25.00
# This originates from X11R5 (mit/util/scripts/install.sh), which was
# later released in X11R6 (xc/config/util/install.sh) with the
# following copyright and license.
#
# Copyright (C) 1994 X Consortium
#
# Permission is hereby ... | Shell |
#! /bin/sh
# Common stub for a few missing GNU programs while installing.
scriptversion=2006-05-10.23
# Copyright (C) 1996, 1997, 1999, 2000, 2002, 2003, 2004, 2005, 2006
# Free Software Foundation, Inc.
# Originally by Fran,cois Pinard <pinard@iro.umontreal.ca>, 1996.
# This program is free software; you can redi... | Shell |
#! /bin/sh
# mkinstalldirs --- make directory hierarchy
scriptversion=2006-05-11.19
# Original author: Noah Friedman <friedman@prep.ai.mit.edu>
# Created: 1993-05-16
# Public domain.
#
# This file is maintained in Automake, please report
# bugs to <bug-automake@gnu.org> or send patches to
# <automake-patches@gnu.org>... | Shell |
#! /bin/sh
# Wrapper for compilers which do not understand `-c -o'.
scriptversion=2005-05-14.22
# Copyright (C) 1999, 2000, 2003, 2004, 2005 Free Software Foundation, Inc.
# Written by Tom Tromey <tromey@cygnus.com>.
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the ... | Shell |
#!/bin/bash
# (1) runs orthAgogue with the correct parameters:
mpirun -np 4 ./orthAgogue -i empirical_tests/goodProteins.blast -w -O empirical_tests/turbo/gp_file/ -b -c 1 -dbs 2000;
# (2) Starts the comparison. (If unsure about what happenning, skip the arguments to the script, and the help will provide the answers!)... | Shell |
#!/bin/bash
# (1) runs orthAgogue with the correct parameters:
#./orthAgogue -i empirical_tests/second_proteins.blast -w -O empirical_tests/files_second/turbo/ -b -c 1;
#! Perform the comparison
perl heuristical_orthology_building/heuristical_orthology_building.pl empirical_tests/second_proteins.blast empirical_tests... | Shell |
#!/bin/bash
module load intelcomp/12.1.0 2>err_mod_load.txt;
scripts_shell/pre-installation.pl bug 20000000
exit; | Shell |
#!/bin/bash
./orthaGogue -c 1 -i all_vm.blast -nss;
mv orthologs.abc cpu_1.orthologs.abc ;
./orthaGogue -c 2 -i all_vm.blast -nss;
wc -l cpu_1.orthologs.abc orthologs.abc ;
exit; | Shell |
#!/bin/bash
module load intelcomp/12.1.0 2>err_mod_load.txt;
module load openmpi/1.4.3
scripts_shell/pre-installation.pl bug 20000000 -DUSE_MPI=1
exit; | Shell |
#!/bin/bash
module load intelcomp/12.1.0 2>err_mod_load.txt;
#scripts_shell/pre-installation.pl remove_configs
#scripts_shell/pre-installation.pl fart 20000000
rm CMakeCache.txt;
cmake -D CMAKE_BUILD_TYPE:STRING=RELEASE -D LOG_FOLDER_NAME:STRING=report_orthAgogue -D MEMORY_CONSUMPTION_LEVEL=1 -D VERSION=-D CPACK_PACKA... | Shell |
#!/bin/sh
#------------------------------------------------------------
# GENERATES THE DOCUMENTATION
#------------------------------------------------------------
doxygen ../Doxyfile;
make -C latex/;
exit; | Shell |
#!/bin/sh
echo""
echo "Runs the script enabling simple debugging, setting the parameters in the CMakeLists.txt-files" ;
# Removes the system-specific cmake-files:
find . -iname "CMakeCache.txt" -exec rm {} \;
#------------------------------------------------------------
# STATUS MESSAGES (Hopefully none file should... | Shell |
#!/bin/bash
#------------------------------------------------------------
# GENERATES THE DOCUMENTATION
#------------------------------------------------------------
CURRENT=`pwd`
BASENAME=`basename $CURRENT`
# Gets the version number by removing the other stuff:
v_number=`echo $BASENAME | sed s/_[a-zA-Z]*_//`;
#doc_p... | Shell |
#!/bin/sh
FIND_STRING="orthaGogue";
REPLACE_STRING="orthAgogue";
ROOT=".";
echo "-\tContinue with FIND_STRING=" $FIND_STRING ", REPLACE_STRING=" $REPLACE_STRING " and ROOT=" $ROOT "? (yes for starting)";
read affirm;
if [ "$affirm" = "yes" ] ; then
echo "-\tStarts operation:" $affirm
else
echo "--\tAborts th... | Shell |
#!/bin/sh
ROOT=".";
# Use the following commands to change file or folder permissions:
# chmod (change file modes)
# chown (change file owner)
# chgrp (change file group owner)
# The following letters represent
# " u " - user/owner
# " g " - group owner
# " o " - all other users
# " a " - for all: user/owner, group ow... | Shell |
#!/bin/sh
#------------------------------------------------------------
# THE CPACK CONFIGURATION chmod
#------------------------------------------------------------
#echo "Runs the cpack configuration."
# FIXME: inkluder nedenfor!
# cmake .;
# # Binary package:
cpack -C CPackConfig.cmake;
# cpack -C CPackConfig.cmak... | Shell |
#!/bin/bash
#------------------------------------------------------------
# GENERATES THE DOCUMENTATION
#------------------------------------------------------------
CURRENT=`pwd`
BASENAME=`basename $CURRENT`
# Gets the version number by removing the other stuff:
v_number=`echo $BASENAME | sed s/_[a-zA-Z]*_//`;
#doc_p... | Shell |
#CURRENT=`pwd`
#BASENAME=`basename $CURRENT`
# Gets the version number by removing the other stuff:
#v_number=`echo $BASENAME | sed s/_[a-zA-Z]*_//`;echo $v_number;
dir_release=$2; #"../$BASENAME.executables";
name_soft=$1;
echo "In 'move_cpacks' dire_release=" $dir_release " name_soft=" $name_soft;
rm -rf $dir_release... | Shell |
#!/bin/sh
#
# Task doing regression testing using Valgrind with a quiet mode:
# Testing the file read on second parsing:
DISK_BUFFER_SIZE="1024";
MEMORY_CONSUMPTION_LEVEL="0"
#--
desc="Testing the file read on second parsing with DISK_BUFFER_SIZE=$DISK_BUFFER_SIZE and MEMORY_CONSUMPTION_LEVEL=$MEMORY_CONSUMPTION_LEVEL... | Shell |
#------------------------------------------------------------
# STATUS MESSAGES (Hopefully none file should be found.)
#------------------------------------------------------------
# Finds the files above 10MB, producing a warning.
find . -type f -size +5000k -exec ls -lh {} \; | awk '{ print "\tConsider removing " $... | Shell |
#!/bin/sh
# Finds the files above 10MB:
find . -type f -size +50000k -exec ls -lh {} \; | awk '{ print $9 ": " $5 }'
# Greps the things to do before release, with highest priority to the FIXME's
grep -H -r "FIXME" *.h
grep -H -r "FIXME" *.cxx
grep -H -r "FIXME" *.txt *.cmake *.sh *.bash
#grep -H -r "TODO" . | Shell |
#------------------------------------------------------------
# REMOVAL OF TEMPORARY FILES:
#------------------------------------------------------------
# Removes the resulting files produced during the oepration:
find . -iname "*.abc" -exec rm -f {} \;
find . -iname "*.mci" -exec rm -f {} \;
find . -iname "*.map" -e... | Shell |
#!/bin/sh
CURRENT=`pwd`
BASENAME=`basename $CURRENT`
v_number=`echo $BASENAME | sed s/[a-zA-Z]*_//`;
#echo "version_number="$v_number;
echo $v_number;
exit; | Shell |
#!/bin/sh
STRING="FIXME";
FOLDER=".";
FILE_TYPES_1="*.h";
if [ "$#" -eq 1 ] ; then
STRING=$1;
else
if [ "$#" -eq 2 ] ; then
STRING=$1;
FOLDER=$2;
else
if [ "$#" -eq 3 ] ; then
STRING=$1;
FOLDER=$2;
FILE_TYPES_1=$3;
fi
fi
fi
echo "Searches in " $FOLDER " of type " $FILE_TYPES_1 " fo... | Shell |
#!/bin/sh
# Create *.png files from text @startuml code and output *.png images to ./doc-src/images folder
# Recusively search from current folder scanning *.c, *.cpp, *.h, and *.doc files
java -Djava.awt.headless=true -jar $PLANTUML_JAR -v -o $PWD/doc-src/images "./**.(c|cpp|doc|h)"
doxygen | Shell |
#!/bin/sh
echo ""
echo "Runs the cpack config."
# Binary package:
cpack -C CPackConfig.cmake
# Source package:
cpack -C CPackSourceConfig.cmake
exit; | Shell |
#!/bin/bash
FIND_STRING="turboOrtho";
REPLACE_STRING="orthaGogue";
ROOT=".";
echo "-\tContinue with FIND_STRING=" $FIND_STRING ", REPLACE_STRING=" $REPLACE_STRING " and ROOT=" $ROOT "? (yes for starting)";
read affirm;
if [ "$affirm" = "yes" ] ; then
echo "-\tStarts operation:" $affirm
else
echo "--\tAborts ... | Shell |
#!/bin/bash
#
# rm *.abc *.mci;
# make 1>out.txt; ./orthAgogue -i empirical_tests/goodProteins.blast --print_blast_filter_data; # > out_without_overlap_thrs.txt
# wc -l *.abc;
# rm *.abc *.mci;
# make 1>out.txt; ./orthAgogue -i empirical_tests/goodProteins.blast --print_blast_filter_data -lc; # > out_without_overlap_... | Shell |
#!/bin/bash
# Sets some properties for the run (easier to use as template then):
FILE_OUT="out_orthaGogue.txt;"
FILE_ERR="err_orthaGogue.txt";
PROGRAM="./orthaGogue";
# Sets the disk buffer size:
B_SIZE=`echo 1024*1024*20 | bc`
cd ..; # Goes one level down getting the correct folder name:
CURRENT=`pwd`
BASENAME=`basena... | Shell |
#!/bin/bash
#./install.bash; ./scripts_shell/pre-installation.pl pre_install;
./scripts_shell/pre-installation.pl pre_install; | Shell |
#!/bin/sh
module load intelcomp; # For centOS
make clean;
exit; | Shell |
# If the out-file is empy it migh imply an error in the running:
#
# FIXME: Does not prodcure error when it should!
if [ -s $FILE_OUT ] ; then
echo "ok Installation completed. You may now run $PROGRAM ;) ";
cat $FILE_OUT;
else
echo "$FILE_OUT is empty. Writes the error";
cat $FILE_ERR;
fi ;
exit; | Shell |
#!/bin/bash
module load intelcomp/12.1.0 2>err_mod_load.txt;
module load openmpi/1.4.3
scripts_shell/pre-installation.pl fart 20000000 -DUSE_MPI=1
exit; | Shell |
#!/bin/sh
./tests_empirical/produce_smaller_file_for_verific.sh;
valgrind --leak-check=full --log-file=valgrind.log ./orthaGogue -i temp.blast -s '|' -t 0 -p 1 -c 1 -O result_folder; | Shell |
#!/bin/bash
# -rwxr-xr-x 1 mironov metacenter 31K May 3 18:32 /norstore/user/mironov/workspace/omcl/omcl2.0.3/sample/goodProteins.blast
# ==> /norstore/user/mironov/workspace/omcl/omcl2.0.3/sample/goodProteins.blast <==
# ath|At1g01190_atath|At1g01190_at100.0053500153515350.01107
# ath|At1g01190_atath|At1g01280_at30... | Shell |
#!/bin/sh
#
#PBS -m abe
#PBS -A acc-biology
#PBS -lwalltime=01:10:00
#PBS -lnodes=1:ppn=1
#PBS -N improved_d
module load intelcomp;
cd /home/olekrie/orthaGogue_0.9.9.0/src;
./orthaGogue -i /work/olekrie/cco-2011-11-17.blast -s '_' -p 0 -t 1 -c 1 -O result_folder ;
#./orthaGogue -i /work/mironov/outputs/blast/HsMmRn.bl... | Shell |
#!/bin/sh
#############################################################
#### Use 'qsub filename' to submit job ####
#### Follow the jobs progress with one of these commands ####
#### 'qstat -a' ####
#### 'watch qstat -a' ####
... | Shell |
#!/bin/sh
#
#PBS -A acc-biology
#PBS -lwalltime=1:10:00
#PBS -lnodes=1:ppn=9
#PBS -N speedy
module load intelcomp/12.1.0;
cd /home/olekrie/orthaGogue_0.9.9.3/src;
#
# Then the debug version in order to compare time and results:
./orthaGogue -i /work/olekrie/cco-2011-11-17.blast -s '_' -p 0 -t 1 -c 1 -O result_folder_... | Shell |
#!/bin/bash
# -rw-r--r-- 1 mironov metacenter 1.9G May 6 18:33 /norstore/user/mironov/workspace/omcl/omcl2.0.3/7-set/goodProteins.blast
PATH="/norstore/user/mironov/workspace/omcl/omcl2.0.3/7-set/goodProteins.blast";
CPU_CNT=1; time ./orthAgogue -i $PATH -nss -o 50 -t 0 -p 1 -s '|' -c $CPU_CNT;
CPU_CNT=2; time ./o... | Shell |
#!/bin/sh
#
#PBS -m abe
#PBS -A acc-biology
#PBS -lwalltime=6:10:00
#PBS -lnodes=1:ppn=9
#PBS -N speedy
module load intelcomp/12.1.0;
cd /home/olekrie/orthaGogue_0.9.9.3/src;
perl scripts_shell/pre-installation.pl fart 10000000 -O result_folder_10mb; # A gigh speed
./orthaGogue -i /work/olekrie/cco-2011-11-17.blast -... | Shell |
#!/bin/bash
# -rw-r--r-- 1 mironov metacenter 11M May 7 12:16 /norstore/user/mironov/workspace/omcl/omcl2.0.3/test/goodProteins.blast
CPU_CNT=4;
# echo $CPU_CNT;
# -rw-r--r-- 1 mironov metacenter 169M May 5 16:31 /norstore/user/mironov/workspace/omcl/omcl2.0.3/4-set/goodProteins.blast
PATH="/norstore/user/mironov/w... | Shell |
#!/bin/sh
#############################################################
#### Use 'qsub filename' to submit job ####
#### Follow the jobs progress with one of these commands ####
#### 'qstat -a' ####
#### 'watch qstat -a' ####
... | Shell |
#!/bin/bash
./orthaGogue -i "/norstore/user/mironov/workspace/omcl/omcl2.0.3/sprot/goodProteins.blast" -nss -o 50 -c 1 -t 0 -p 1 -s '|'
| Shell |
#!/bin/sh
#
#PBS -m abe
#PBS -A acc-biology
#PBS -lwalltime=0:40:00
#PBS -lnodes=1:ppn=1
#PBS -N tsec_ser_n
module load intelcomp/12.1.0;
cd /home/olekrie/orthaGogue_0.9.9.3/src;
#./orthaGogue -i /work/olekrie/cco-2011-11-17.blast -s '_' -p 0 -t 1 -c 1 -O result_folder_1
./orthaGogue -i /work/olekrie/cco-2011-11-17.bl... | Shell |
#!/bin/sh
#############################################################
#### Use 'qsub filename' to submit job ####
#### Follow the jobs progress with one of these commands ####
#### 'qstat -a' ####
#### 'watch qstat -a' ####
... | Shell |
#
#PBS -m abe
#PBS -A acc-biology
#PBS -lwalltime=08:10:00
#PBS -lnodes=1:ppn=1
#PBS -N valgrind
module load intelcomp/12.1.0;
cd /home/olekrie/orthaGogue_0.9.9.3/src;
valgrind --track-origins=yes ./orthaGogue -i /work/olekrie/cco-2011-11-17.blast -s '_' -p 0 -t 1 -c 1 -O result_folder ; | Shell |
#!/bin/sh | Shell |
#!/bin/sh
#############################################################
#### Use 'qsub filename' to submit job ####
#### Follow the jobs progress with one of these commands ####
#### 'qstat -a' ####
#### 'watch qstat -a' ####
... | Shell |
#!/bin/bash
# -rw-r--r-- 1 mironov metacenter 1.9G May 6 18:33 /norstore/user/mironov/workspace/omcl/omcl2.0.3/7-set/goodProteins.blast
PATH="/norstore/user/mironov/workspace/omcl/omcl2.0.3/7-set/goodProteins.blast";
CPU_CNT=5;
echo $CPU_CNT;
time ./orthaGogue -i $PATH -nss -o 50 -t 0 -p 1 -s '|' -c $CPU_CNT;
echo... | Shell |
#!/bin/sh
#
#PBS -A acc-biology
#PBS -lwalltime=4:10:00
#PBS -lnodes=1:ppn=9
#PBS -N speedy_8
module load intelcomp/12.1.0;
module load cmake/2.8.7cmake/2.8.7
cd /home/olekrie/orthaGogue_0.9.9.3/src;
#
# Then the debug version in order to compare time and results:
valgrind --leak-check=full --log-file=valgrind_8.log ... | Shell |
#!/bin/sh
#
#PBS -m abe
#PBS -A acc-biology
#PBS -lwalltime=0:40:00
#PBS -lnodes=1:ppn=7
#PBS -N opt_7
module load intelcomp/12.1.0;
cd /home/olekrie/orthaGogue_0.9.9.5;
#PATH="/work/olekrie/goodProteins.blast";
./orthaGogue -i /work/olekrie/goodProteins.blast -nss -o 50 -t 0 -p 1 -s '|' -O result_folder -c 1 ;
./ort... | Shell |
#!/bin/sh
#
#PBS -m abe
#
# The queuing system will send an email on job Abort, Begin, End
#
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
#
#PBS -A acc-biology
###PBS -q routine
###PBS -q express
#PBS -lwalltime=06:30:00
#PBS -lnodes=1:ppn=10
#PBS -N read_with_o2
##PBS -N second_pipe_fr... | Shell |
#!/bin/sh
#
#PBS -m abe
#PBS -A acc-biology
#PBS -lwalltime=08:10:00
#PBS -lnodes=1:ppn=1
#PBS -N valgrind
module load intelcomp/12.1.0;
cd /home/olekrie/orthaGogue_0.9.9.3/src;
valgrind --track-origins=yes ./orthaGogue -i /work/olekrie/cco-2011-11-17.blast -s '_' -p 0 -t 1 -c 1 -O result_folder ;
wc -l result_folder/... | Shell |
#!/bin/sh
#############################################################
#### Use 'qsub filename' to submit job ####
#### Follow the jobs progress with one of these commands ####
#### 'qstat -a' ####
#### 'watch qstat -a' ####
... | Shell |
#!/bin/sh
#
#PBS -m abe
#PBS -A acc-biology
#PBS -lwalltime=01:10:00
#PBS -lnodes=1:ppn=1
#PBS -N valgrind
module load intelcomp/12.1.0;
cd /home/olekrie/orthaGogue_0.9.9.3/src;
#perl scripts_shell/pre-installation.pl bug 20000000
valgrind --track-origins=yes ./orthaGogue -i empirical_tests/goodProteins.blast -nn -c 1... | Shell |
#!/bin/sh
#------------------------------------------------------------
# GENERATES THE DOCUMENTATION
#------------------------------------------------------------
doxygen ../Doxyfile;
make -C latex/;
exit; | Shell |
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