| Miscellaneous |
| Version lineage of this tool (guids ordered most recent to oldest) |
| toolrepo.galaxytrakr.org/repos/jpayne/snp_pipeline/call_sites/1.0.1 (this tool) |
| call_sites |
| Requirements (dependencies defined in the <requirements> tag set) |
| name | version | type |
| bowtie2 | 2.3.5 | package |
| samtools | 1.9 | package |
| bzip2 | 1.0.6 | package |
| picard | not provided | package |
| varscan | not provided | package |
| boto3 | 1.9.134 | package |
| python | 3.6.8 | package |
| Additional information about this tool |
export LD_LIBRARY_PATH="\$CONDA_DEFAULT_ENV/lib" &&
python $__tool_directory__/snp-cache.py snp_sitecalls
"\$(md5sum $input $sample | cut -c -32 | md5sum | cut -c -32)"
-c "
cp $input ./reference.fasta &&
samtools faidx ./reference.fasta &&
samtools view -bS -F 4 $sample |
samtools sort -o ./sorted.bam - &&
picard MarkDuplicates INPUT=./sorted.bam
OUTPUT=/dev/stdout
METRICS_FILE=./metrics |
samtools mpileup -f ./reference.fasta - -o ./pileup
&&
varscan mpileup2snp ./pileup
--min_var-freq 0.90
--output-vcf 1
> ./calls
&& tar -zcf /dev/stdout ./metrics ./pileup ./calls
"
-o ./archive.tar.gz
-l $cache_log
&& cat $cache_log
&& tar -zxvf ./archive.tar.gz
&& cp ./metrics $metrics
&& cp ./pileup $pileup
&& cp ./calls $calls
| Functional tests |
| name | inputs | outputs | required files |
| Test-1 |
sample: samples/sample2/reads.sam input: reference/lambda_virus.fasta |
attributes: name attributes: name |
reference/lambda_virus.fasta samples/sample2/reads.sam name |