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[TOOLS]
; Tool Configuration
;
; Some tools require additional files or might require a hard coded path to the script.
; Please make sure these are set up correctly.
; Trimmomatic Path
; ADJUST THIS
trimmomatic_path=/home/sepro/tools/Trimmomatic-0.36/trimmomatic-0.36.jar
; COMMANDS to run tools
;
; Here the commands used to start different steps are defined, ${name} are variables that will be set by LSTrAP for
; each job.
; Note that in some cases hard coded paths were required, adjust these to match the location of these files on
; your system
bowtie_cmd=bowtie2-build ${in} ${out}
hisat2_build_cmd=hisat2-build ${in} ${out}
; ADJUST PATHS TO ADAPTERS
trimmomatic_se_command=java -jar ${jar} SE -threads 1 ${in} ${out} ILLUMINACLIP:/home/sepro/tools/Trimmomatic-0.36/adapters/TruSeq3-SE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36
trimmomatic_pe_command=java -jar ${jar} PE -threads 1 ${ina} ${inb} ${outap} ${outau} ${outbp} ${outbu} ILLUMINACLIP:/home/sepro/tools/Trimmomatic-0.36/adapters/TruSeq3-PE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36
tophat_se_cmd=tophat -p 3 -o ${out} ${genome} ${fq}
tophat_pe_cmd=tophat -p 3 -o ${out} ${genome} ${forward},${reverse}
hisat2_se_cmd=hisat2 -p 3 -x ${genome} -U ${fq} -S ${out} 2> ${stats}
hisat2_pe_cmd=hisat2 -p 3 -x ${genome} -1 ${forward} -2 ${reverse} -S ${out} 2> ${stats}
htseq_count_cmd=htseq-count -s no -f ${itype} -t ${feature} -i ${field} ${bam} ${gff} > ${out}
interproscan_cmd=interproscan.sh -i ${in_dir}/${in_prefix}${SGE_TASK_ID} -o ${out_dir}/${out_prefix}${SGE_TASK_ID} -f tsv -dp -iprlookup -goterms --tempdir /tmp
pcc_cmd=python3 ./scripts/pcc.py ${in} ${out} ${mcl_out}
mcl_cmd=mcl ${in} --abc -o ${out} -te 4
; ADJUST THIS
mcxdeblast_cmd=perl /apps/biotools/mcl-14.137/bin/mcxdeblast --m9 --line-mode=abc ${blast_in} > ${abc_out}
; ADJUST THIS
orthofinder_cmd=python /home/sepro/OrthoFinder-0.4/orthofinder.py -f ${fasta_dir} -t 8
; qsub parameters (OGE)
qsub_indexing=''
qsub_trimmomatic=''
qsub_tophat='-pe cores 4'
qsub_htseq_count=''
qsub_interproscan='-pe cores 5'
qsub_pcc=''
qsub_mcl='-pe cores 4'
qsub_orthofinder='-pe cores 8'
qsub_mcxdeblast=''
; qsub parameters (PBS/Torque)
; qsub_indexing=''
; qsub_trimmomatic=''
; qsub_tophat='-l nodes=1,ppn=4'
; qsub_htseq_count=''
; qsub_interproscan='-l nodes=1,ppn=5'
; qsub_pcc=''
; qsub_mcl='-l nodes=1,ppn=4'
; qsub_orthofinder='-l nodes=1,ppn=8'
; qsub_mcxdeblast=''
; qsub parameters (PBS/Torque with walltimes)
; qsub_indexing='-l walltime=00:10:00'
; qsub_trimmomatic='-l walltime=00:10:00'
; qsub_tophat='-l nodes=1,ppn=4 -l walltime=00:10:00'
; qsub_htseq_count=' -l walltime=00:02:00'
; qsub_interproscan='-l nodes=1,ppn=5 -l walltime=00:10:00'
; qsub_pcc=' -l walltime=00:10:00'
; qsub_mcl='-l nodes=1,ppn=4 -l walltime=00:10:00'
; qsub_orthofinder='-l nodes=1,ppn=8 -l walltime=01:00:00'
; qsub_mcxdeblast='-l walltime=00:10:00'
; Module names
; These need to be configured if the required tools are installed in the environment modules.
; You can find the modules installed on your system using
;
; module avail
;
; In case there is no module load system on the system set the module name to None
bowtie_module=biotools/bowtie2-2.2.6
samtools_module=biotools/samtools-1.3
sratoolkit_module=biotools/sratoolkit-2.5.7
tophat_module=biotools/tophat-2.1.0
hisat2_module=biotools/hisat2-2.1.0
interproscan_module=biotools/interproscan-5.16-55.0
blast_module=biotools/ncbi-blast-2.3.0+
mcl_module=biotools/mcl-14.137
python_module=devel/Python-2.7.10
python3_module=devel/Python-3.5.1