/usr/bin/crac-client is in crac 2.5.0+dfsg-2.
This file is owned by root:root, with mode 0o755.
The actual contents of the file can be viewed below.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 | #!/bin/bash
###############################################################################
# #
# #
# Copyright © 2010-2012 -- LIRMM/CNRS #
# (Laboratoire d'Informatique, de Robotique et de #
# Microélectronique de Montpellier / #
# Centre National de la Recherche Scientifique). #
# LIFL/INRIA #
# (Laboratoire d'Informatique, du Traitement de #
# l'Information et des Systèmes) #
# #
# Auteurs/Authors: CRAC list <crac-bug@gforge.inria.fr> #
# Nicolas PHILIPPE <nicolas.philippe@lirmm.fr> #
# Mikaël SALSON <mikael.salson@lifl.fr> #
# Thérèse COMMES <therese.commes@univ-montp2.fr> #
# Éric RIVALS <eric.rivals@lirmm.fr> #
# Alban MANCHERON <alban.mancheron@lirmm.fr> #
# #
# ------------------------------------------------------------------------- #
# #
# Ce fichier fait partie du programme CRAC. #
# #
# Crac est un outil d'analyse de données de RNA-Seq provenant des NGS. #
# #
# Ce logiciel est régi par la licence CeCILL soumise au droit français et #
# respectant les principes de diffusion des logiciels libres. Vous pouvez #
# utiliser, modifier et/ou redistribuer ce programme sous les conditions de #
# la licence CeCILL telle que diffusée par le CEA, le CNRS et l'INRIA sur #
# le site "http://www.cecill.info". #
# #
# En contrepartie de l'accessibilité au code source et des droits de copie, #
# de modification et de redistribution accordés par cette licence, il n'est #
# offert aux utilisateurs qu'une garantie limitée. Pour les mêmes raisons, #
# seule une responsabilité restreinte pèse sur l'auteur du programme, le #
# titulaire des droits patrimoniaux et les concédants successifs. #
# #
# À cet égard l'attention de l'utilisateur est attirée sur les risques #
# associés au chargement, à l'utilisation, à la modification et/ou au #
# développement et à la reproduction du logiciel par l'utilisateur étant #
# donné sa spécificité de logiciel libre, qui peut le rendre complexe à #
# manipuler et qui le réserve donc à des développeurs et des professionnels #
# avertis possédant des connaissances informatiques approfondies. Les #
# utilisateurs sont donc invités à charger et tester l'adéquation du #
# logiciel à leurs besoins dans des conditions permettant d'assurer la #
# sécurité de leurs systêmes et ou de leurs données et, plus généralement, #
# à l'utiliser et l'exploiter dans les mêmes conditions de sécurité. #
# #
# Le fait que vous puissiez accéder à cet en-tête signifie que vous avez #
# pris connaissance de la licence CeCILL, et que vous en avez accepté les #
# termes. #
# #
# ------------------------------------------------------------------------- #
# #
# This File is part of the CRAC program. #
# #
# Crac is a tool to analyse RNA-Seq data provided by NGS. #
# #
# This software is governed by the CeCILL license under French law and #
# abiding by the rules of distribution of free software. You can use, #
# modify and/ or redistribute the software under the terms of the CeCILL #
# license as circulated by CEA, CNRS and INRIA at the following URL #
# "http://www.cecill.info". #
# #
# As a counterpart to the access to the source code and rights to copy, #
# modify and redistribute granted by the license, users are provided only #
# with a limited warranty and the software's author, the holder of the #
# economic rights, and the successive licensors have only limited #
# liability. #
# #
# In this respect, the user's attention is drawn to the risks associated #
# with loading, using, modifying and/or developing or reproducing the #
# software by the user in light of its specific status of free software, #
# that may mean that it is complicated to manipulate, and that also #
# therefore means that it is reserved for developers and experienced #
# professionals having in-depth computer knowledge. Users are therefore #
# encouraged to load and test the software's suitability as regards their #
# requirements in conditions enabling the security of their systems and/or #
# data to be ensured and, more generally, to use and operate it in the same #
# conditions as regards security. #
# #
# The fact that you are presently reading this means that you have had #
# knowledge of the CeCILL license and that you accept its terms. #
# #
###############################################################################
PIPE=`dirname $0`/classify.fifo
PIPE_OUT=`dirname $0`/classify.out.fifo
MAX_NB_ITER=100 # 100s
if [ $# -gt 5 -o "$1" == "-h" -o "$1" == "--help" ]
then
echo "Usage: $0 [-in <input_pipe>] [-out <output_pipe>] [-q]" >&2
exit 1
fi
QUIET=0
while [ $# -gt 0 ]
do
if [ "$1" == "-in" ]; then
PIPE=$2
shift
elif [ "$1" == "-out" ]; then
PIPE_OUT=$2
shift
elif [ "$1" == "-q" ]; then
QUIET=1
else
echo "Unknown option $1" >&2
fi
shift
done
if [ $QUIET -eq 0 ]; then
echo "This is the client of crac v. 2.5.0";
fi
[ -p $PIPE ] || PIPE=${PIPE/`dirname $0`/$PWD}
[ -p $PIPE_OUT ] || PIPE_OUT=${PIPE_OUT/`dirname $0`/$PWD}
if [ ! -p $PIPE -o ! -p $PIPE_OUT ]
then
echo "$PIPE or $PIPE_OUT does not exist... Maybe you didn't launch crac --server?"
exit 1
fi
# Connecting
echo -n "connect@$$" > $PIPE
cat $PIPE_OUT > /dev/null
SUBPIPE=`dirname $0`/in.$$.fifo
SUBPIPE_OUT=`dirname $0`/out.$$.fifo
NB_ITER=0
[ -p $SUBPIPE ] || SUBPIPE=${SUBPIPE/`dirname $0`/`dirname $PIPE`}
[ -p $SUBPIPE_OUT ] || SUBPIPE_OUT=${SUBPIPE_OUT/`dirname $0`/`dirname $PIPE_OUT`}
while [ ! -p $SUBPIPE_OUT -a $NB_ITER -le $MAX_NB_ITER ]; do
sleep 0.1s
NB_ITER=$((NB_ITER+1))
done
if [ $NB_ITER -ge $MAX_NB_ITER ]; then
echo "Oops! Output pipe was not created.
Maybe it has not been created in the directory I expected.
Something going wrong, I'm leaving cowardly." >&2
exit 2
fi
if [ $QUIET -eq 0 ]; then
echo -n "> "
fi
while read line; do
set -- $line
PRINT=0
if [ "$1" == "help" ]; then
echo "* Set a variable: set <variable> <value>
* Locate a pattern: locate <pattern>
* Locate each k-mer in a sequence: klocate <k> <dna sequence>
* Get information about a read: <read id>
* Get information about a read (with its name): name <read name>
* Get reads sharing the same k-factor as the one at position <pos> in <read id>: <read id>:<pos>
* Get reads sharing a given factor: tag <factor>
* Get reads that have a given factor at a given position: tag pos <position> <factor>
* Retrieve a genome factor: genome [reverse] <chr_name:position> <length>
* Get GkSA value: GkSA <pos>
* Quit main server: quit
* Quit only child server: <Ctrl>+D"
elif [ "$1" != "" -a "${1:0:1}" != ">" -a "${1:0:1}" != "#" ]; then
while [ $# -gt 0 ]; do
if [ "$1" == "set" -a $# -ge 3 ]
then
echo -n "set|$2|$3" > $SUBPIPE
shift 3
elif [ "$1" == "name" -a $# -ge 2 ]; then
echo -n "name|$2" > $SUBPIPE
shift 2
elif [ "$1" == "locate" -a $# -ge 2 ]; then
echo -n "loc|"`expr length $2`"|$2" > $SUBPIPE
shift 2
elif [ "$1" == "klocate" -a $# -ge 3 ]; then
k=$2
seq=$3
for (( i=0 ; $i < $((${#seq}-k+1)); i++ )); do
echo -n "loc|$k|"${seq:$i:$k} > $SUBPIPE
cat $SUBPIPE_OUT
done
PRINT=1
shift 3
elif [ "$1" == "tag" -a $# -ge 4 -a "$2" == "pos" ]; then
echo -n "tag|"`expr length $4`"|$4" > $SUBPIPE
cat $SUBPIPE_OUT | grep -Ewo "[0-9]+:$3" | awk -F: '{print $1}'
shift 4
PRINT=1
elif [ "$1" == "tag" -a $# -ge 2 ]; then
echo -n "tag|"`expr length $2`"|$2" > $SUBPIPE
shift 2
elif [ "$1" == "GkSA" -a $# -ge 2 ]; then
echo -n "GkSA|$2" > $SUBPIPE
shift 2
elif [ "$1" == "genome" -a $# -ge 3 ]; then
if [ "$2" == "reverse" ]; then
REV="true"
shift
else
REV="false"
fi
if [[ $2 == *:* ]]; then
chr=$(echo $2 | cut -d: -f1)
pos=$(echo $2 | cut -d: -f2)
if [ "$REV" == "true" ]; then
pos=-$pos
fi
echo -n "genome|$chr|$pos|$3" > $SUBPIPE
else
echo "Missing ``:''" >&2
fi
shift 3
elif [ "$1" == "quit" ]; then
echo -n "q" > $SUBPIPE
cat $SUBPIPE_OUT
echo -n "q" > $PIPE
cat $PIPE_OUT
exit 0
elif [ "$1" == "print" ]; then
shift
echo $*
shift $#
PRINT=1
elif [[ "$1" =~ ^[0-9]+$ ]] || [[ "$1" =~ ^[0-9]+:[0-9]+$ ]]; then
echo -n "$1" > $SUBPIPE
shift
else
echo "Unkown command."
shift
PRINT=1
fi
if [ $PRINT -eq 0 ]; then
cat $SUBPIPE_OUT
fi
done
fi
if [ $QUIET -eq 0 ]; then
echo -n "> "
fi
done
if [ $QUIET -eq 0 ]; then
echo
fi
echo -n "q" > $SUBPIPE
cat $SUBPIPE_OUT > /dev/null
|