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Samtools location #25

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6f22dc8
Calling samtools from within the msg directory
tinathu Feb 9, 2012
372a430
Added version checking for samtools dependency
lparsons Feb 9, 2012
b891f39
Updated installation instructions for local samtools installation
lparsons May 2, 2012
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1 change: 1 addition & 0 deletions README
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Original file line number Diff line number Diff line change
Expand Up @@ -16,6 +16,7 @@ R packages (HiddenMarkov 1.3-1, zoo 1.6-2, R.methodsS3 1.2.0 and R.oo 1.7.3)
### Installation instructions ###
git clone git://github.com/JaneliaSciComp/msg.git
cd msg
copy or link version 0.1.9 of samtools into the msg directory
make

### Toy Example ###
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14 changes: 8 additions & 6 deletions make-pileups.sh
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Expand Up @@ -17,6 +17,8 @@ true=0
false="false"

all=$false
script_dir=$(dirname $0)


while getopts "ai:d:p:q:" opt
do
Expand Down Expand Up @@ -44,19 +46,19 @@ species=par1
file=$dir/aln_${indiv}_${species}-filtered
echo "$file"

[ -e $parent1.fai ] || samtools faidx $parent1
[ -e $parent1.fai ] || $script_dir/samtools faidx $parent1
[ -e $file-sorted.bam ] || {
echo "samtools view -bt $parent1.fai $file.sam | samtools sort - $file-sorted"
samtools view -bt $parent1.fai $file.sam | samtools sort - $file-sorted
$script_dir/samtools view -bt $parent1.fai $file.sam | $script_dir/samtools sort - $file-sorted
}
[ -e $file-sorted.bam.bai ] || samtools index $file-sorted.bam
[ -e $file-sorted.bam.bai ] || $script_dir/samtools index $file-sorted.bam

for ref in $refs ; do
[ -e $file-$ref-sorted.pileup ] || {
echo "Making pileup for $species contig $ref"
samtools view -bu $file-sorted.bam $ref | samtools sort - $file-$ref-sorted
samtools index $file-$ref-sorted.bam
samtools pileup -cf $parent1 $file-$ref-sorted.bam > $file-$ref-sorted.pileup
$script_dir/samtools view -bu $file-sorted.bam $ref | samtools sort - $file-$ref-sorted
$script_dir/samtools index $file-$ref-sorted.bam
$script_dir/samtools pileup -cf $parent1 $file-$ref-sorted.bam > $file-$ref-sorted.pileup
rm $file-$ref-sorted.bam $file-$ref-sorted.bam.bai
}
done
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14 changes: 7 additions & 7 deletions msg.pl
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Expand Up @@ -16,8 +16,8 @@ sub system_call {

GetOptions(
'barcodes|b=s' => \$barcodes,
're_cutter=s' => \$re_cutter,
'linker_system=s' => \$linker_system,
're_cutter=s' => \$re_cutter,
'linker_system=s' => \$linker_system,
'reads|i=s' => \$raw_read_data,
'update|u' => \$update_genomes,
'parent1=s' => \$parent1_genome,
Expand Down Expand Up @@ -116,7 +116,7 @@ sub system_call {

&system_call("bwa", "index", "-a", $genome_index{$sp}, "$genomes_fa{$sp}.msg")
unless( -e "$genomes_fa{$sp}.msg.bwt" and -e "$genomes_fa{$sp}.msg.ann" );
&system_call("samtools", "faidx", "$genomes_fa{$sp}.msg") ;
&system_call("$src/samtools", "faidx", "$genomes_fa{$sp}.msg") ;

unless (-e "$out.sam") {
&system_call("bwa", "aln", "-t", $update_nthreads, "$genomes_fa{$sp}.msg", $reads_for_updating_fq{$sp}, "> $out.sai") ;
Expand All @@ -125,10 +125,10 @@ sub system_call {

&system_call("$src/filter-sam.py", "-i", "$out.sam", "-o", "$out.filtered.sam") ;

&system_call("samtools", "view", "-bt", "$genomes{$sp}.msg.fai", "-o $out.bam", "$out.filtered.sam") ;
&system_call("samtools", "sort", "$out.bam", "$out.bam.sorted") ;
&system_call("samtools", "index", "$out.bam.sorted.bam") ;
&system_call("samtools", "pileup", "-f", "$genomes_fa{$sp}.msg", "$out.bam.sorted.bam", "-c", "> $out.pileup") ;
&system_call("$src/samtools", "view", "-bt", "$genomes{$sp}.msg.fai", "-o $out.bam", "$out.filtered.sam") ;
&system_call("$src/samtools", "sort", "$out.bam", "$out.bam.sorted") ;
&system_call("$src/samtools", "index", "$out.bam.sorted.bam") ;
&system_call("$src/samtools", "pileup", "-f", "$genomes_fa{$sp}.msg", "$out.bam.sorted.bam", "-c", "> $out.pileup") ;

}

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12 changes: 9 additions & 3 deletions test_dependencies_executable.sh
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Expand Up @@ -20,9 +20,15 @@ if ! which bwa >/dev/null 2>/dev/null ; then
exit 1
fi

if ! which samtools >/dev/null 2>/dev/null ; then
echo "Please install samtools somewhere in your PATH"
exit 1
samtools_required_version="Version: 0.1.9 (r783)"
if ! [ -e $(dirname $0)/samtools ] ; then
echo "Please install samtools ($samtools_required_version) within the msg directory"
exit 1
fi
samtools_version=`$(dirname $0)/samtools 2>&1 | grep 'Version:'`
if [ "$samtools_version" != "$samtools_required_version" ] ; then
echo "The samtools found within the msg directory is $samtools_version. It must be $samtools_required_version"
exit 1
fi

echo "All required executables found in PATH"
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