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Added GPL text to each file.

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commit 8a0195e2ca386ff07736fdf892cdd3307b3682e2 1 parent 76c17a7
@sgivan authored
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18 bin/RNAseq.sh
@@ -3,7 +3,23 @@
# This bash script runs the program "tophat" on a series of fastq
# files of short read sequences
#
-# copyright Scott Givan, The University of Missouri, November 11, 2011.
+# copyright Scott Givan, The University of Missouri, July 6, 2012
+#
+# This file is part of the RNA-seq Toolkit, or RST.
+#
+# RST is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# RST is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with RST. If not, see <http://www.gnu.org/licenses/>.
+#
#
# set path to find RNAseq scripts
wd=`pwd`
View
17 bin/RNAseq_process_data.qsub
@@ -1,4 +1,21 @@
#!/bin/bash
+# copyright Scott Givan, The University of Missouri, July 6, 2012
+#
+# This file is part of the RNA-seq Toolkit, or RST.
+#
+# RST is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# RST is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with RST. If not, see <http://www.gnu.org/licenses/>.
+#
#$ -o $HOME/cluster/output
#$ -e $HOME/cluster/error
View
17 bin/RNAseq_process_data.sh
@@ -1,5 +1,22 @@
#!/bin/bash
#
+# copyright Scott Givan, The University of Missouri, July 6, 2012
+#
+# This file is part of the RNA-seq Toolkit, or RST.
+#
+# RST is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# RST is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with RST. If not, see <http://www.gnu.org/licenses/>.
+#
# run this script from directory containing flowcell directories; ie, the one containing all the FCXXX directories
# then, invoke like FGMG_process_data.sh FC???/s_?
wd=`pwd`
View
17 bin/adapter_trim.pl
@@ -1,4 +1,21 @@
#!/usr/bin/env perl
+# copyright Scott Givan, The University of Missouri, July 6, 2012
+#
+# This file is part of the RNA-seq Toolkit, or RST.
+#
+# RST is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# RST is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with RST. If not, see <http://www.gnu.org/licenses/>.
+#
#
# copyright Scott Givan, University of Missouri, 2010
#
View
17 bin/cc_gtf.pl
@@ -1,4 +1,21 @@
#!/usr/bin/env perl
+# copyright Scott Givan, The University of Missouri, July 6, 2012
+#
+# This file is part of the RNA-seq Toolkit, or RST.
+#
+# RST is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# RST is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with RST. If not, see <http://www.gnu.org/licenses/>.
+#
#
# Copyright 2012 Scott A. Givan
#
View
17 bin/count_mapped_reads_gff.sh
@@ -1,4 +1,21 @@
#!/bin/bash
+# copyright Scott Givan, The University of Missouri, July 6, 2012
+#
+# This file is part of the RNA-seq Toolkit, or RST.
+#
+# RST is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# RST is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with RST. If not, see <http://www.gnu.org/licenses/>.
+#
file=$1
if [ $# != 1 ] ; then
View
17 bin/cuff_sam_to_gff.pl
@@ -1,4 +1,21 @@
#!/usr/bin/env perl
+# copyright Scott Givan, The University of Missouri, July 6, 2012
+#
+# This file is part of the RNA-seq Toolkit, or RST.
+#
+# RST is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# RST is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with RST. If not, see <http://www.gnu.org/licenses/>.
+#
#
use strict;
use Getopt::Long;
View
17 bin/cuffdiff_biomart.pl
@@ -1,5 +1,22 @@
#!/bin/env perl
+# copyright Scott Givan, The University of Missouri, July 6, 2012
+#
+# This file is part of the RNA-seq Toolkit, or RST.
+#
+# RST is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# RST is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with RST. If not, see <http://www.gnu.org/licenses/>.
+#
use 5.010; # Require at least Perl version 5.8
use strict; # Must declare all variables before using them
use warnings; # Emit helpful warnings
View
17 bin/fastq2fasta.sh
@@ -1,3 +1,20 @@
#!/bin/bash
+# copyright Scott Givan, The University of Missouri, July 6, 2012
+#
+# This file is part of the RNA-seq Toolkit, or RST.
+#
+# RST is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# RST is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with RST. If not, see <http://www.gnu.org/licenses/>.
+#
#grep -A 1 "^@\S+\s" $1 | grep -v "^--" | sed "s/^@/>/"
echo 'this script should not be used'
View
17 bin/fastq_pe_matchup.pl
@@ -1,5 +1,22 @@
#!/usr/bin/env perl
#
+# copyright Scott Givan, The University of Missouri, July 6, 2012
+#
+# This file is part of the RNA-seq Toolkit, or RST.
+#
+# RST is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# RST is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with RST. If not, see <http://www.gnu.org/licenses/>.
+#
use 5.8.8;
use strict;
use Getopt::Long;
View
17 bin/fix_cigar.sh
@@ -1,4 +1,21 @@
#!/bin/bash
+# copyright Scott Givan, The University of Missouri, July 6, 2012
+#
+# This file is part of the RNA-seq Toolkit, or RST.
+#
+# RST is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# RST is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with RST. If not, see <http://www.gnu.org/licenses/>.
+#
file=$1
if [ $# != 1 ]
View
17 bin/gffGetmRNA.pl
@@ -4,6 +4,23 @@
#
# Mario Stanke, January, 2010
#
+# copyright Scott Givan, The University of Missouri, July 6, 2012
+#
+# This file is part of the RNA-seq Toolkit, or RST.
+#
+# RST is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# RST is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with RST. If not, see <http://www.gnu.org/licenses/>.
+#
use strict;
use Getopt::Long;
View
17 bin/preprocess.qsub
@@ -1,4 +1,21 @@
#!/bin/bash
+# copyright Scott Givan, The University of Missouri, July 6, 2012
+#
+# This file is part of the RNA-seq Toolkit, or RST.
+#
+# RST is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# RST is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with RST. If not, see <http://www.gnu.org/licenses/>.
+#
#$ -o $HOME/cluster/output
#$ -e $HOME/cluster/error
View
17 bin/preprocess_fq.sh
@@ -1,4 +1,21 @@
#!/bin/bash
+# copyright Scott Givan, The University of Missouri, July 6, 2012
+#
+# This file is part of the RNA-seq Toolkit, or RST.
+#
+# RST is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# RST is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with RST. If not, see <http://www.gnu.org/licenses/>.
+#
#export PATH="~/projects/RNAseq/bin/:$PATH"
wd=`pwd`
osname=`uname -s`
View
17 bin/transcript_filter.pl
@@ -1,5 +1,22 @@
#!/usr/bin/env perl
#
+# copyright Scott Givan, The University of Missouri, July 6, 2012
+#
+# This file is part of the RNA-seq Toolkit, or RST.
+#
+# RST is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# RST is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with RST. If not, see <http://www.gnu.org/licenses/>.
+#
use strict;
use warnings;
use Getopt::Long;
View
18 gpl_text.txt
@@ -0,0 +1,18 @@
+#
+# Copyright Scott A. Givan, University of Missouri, July 6, 2012.
+#
+# This file is part of the RNA-seq Toolkit, or RST.
+#
+# RST is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# RST is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with RST. If not, see <http://www.gnu.org/licenses/>.
+#
View
18 test/TestData_1/setup_and_test.sh
@@ -1,4 +1,22 @@
#!/bin/bash
+#
+# Copyright Scott A. Givan, University of Missouri, July 6, 2012.
+#
+# This file is part of the RNA-seq Toolkit, or RST.
+#
+# RST is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# RST is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with RST. If not, see <http://www.gnu.org/licenses/>.
+#
echo "creating symbolic link to RNAseq tools directory"
ln -s ../../bin ./
View
18 test/TestData_2/setup_and_test.sh
@@ -1,4 +1,22 @@
#!/bin/bash
+#
+# Copyright Scott A. Givan, University of Missouri, July 6, 2012.
+#
+# This file is part of the RNA-seq Toolkit, or RST.
+#
+# RST is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# RST is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with RST. If not, see <http://www.gnu.org/licenses/>.
+#
echo "creating symbolic link to RNAseq tools directory"
ln -s ../../bin ./
View
18 test/TestData_3/setup_and_test.sh
@@ -1,4 +1,22 @@
#!/bin/bash
+#
+# Copyright Scott A. Givan, University of Missouri, July 6, 2012.
+#
+# This file is part of the RNA-seq Toolkit, or RST.
+#
+# RST is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# RST is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with RST. If not, see <http://www.gnu.org/licenses/>.
+#
echo "creating symbolic link to RNAseq tools directory"
ln -s ../../bin ./
View
17 test/run_all_test.sh
@@ -1,4 +1,21 @@
#!/bin/bash
+# copyright Scott Givan, The University of Missouri, July 6, 2012
+#
+# This file is part of the RNA-seq Toolkit, or RST.
+#
+# RST is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# RST is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with RST. If not, see <http://www.gnu.org/licenses/>.
+#
echo 'Running all tests.'
for dir in `ls -1d TestData_*`
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