Commit 2e150236 authored by Penom Nom's avatar Penom Nom
Browse files

Add softwares for gene_diversity.

parent 213b0f2e
......@@ -51,13 +51,16 @@ tmp_directory = <path>/tmp
# uncomment and set if not in the PATH
#blastall = /usr/bin/blastall
#formatdb = /usr/bin/formatdb
#blastn = /usr/bin/blastn
#blastx = /usr/bin/blastx
#makeblastdb = /usr/bin/makeblastdb
#sfffile = /usr/bin/sfffile
#fastqc = /nosave/software/fastqc/current/fastqc
#runAssembly = /usr/bin/runAssembly
#bwa = /usr/bin/bwa
#samtools = /usr/bin/samtools
#ktImportBLAST = /usr/local/bin/ktImportBLAST
#blastn = /usr/bin/blastn
#ktImportText = /usr/local/bin/ImportText.pl
#fastq_illumina_filter = /usr/bin/fastq_illumina_filter
#CollectInsertSizeMetrics = /usr/bin/CollectInsertSizeMetrics.jar
#MarkDuplicates = /usr/bin/MarkDuplicates.jar
......@@ -77,6 +80,9 @@ tmp_directory = <path>/tmp
#bismark_genome_preparation = /nosave/software/bismark_v0.8.3/bismark_genome_preparation
#bismark_methylation_extractor = /nosave/software/bismark_v0.8.3/bismark_methylation_extractor
#fastx_reverse_complement = /usr/bin/fastx_reverse_complement
#framebot = /usr/bin/FrameBot.jar
#usearch = /usr/bin/usearch
#cdhit = /usr/bin/cd-hit
#gaas = /usr/bin/gaas
# Set cluster parameters to some components
......
......@@ -216,7 +216,7 @@ class Cdhit (Analysis):
tmp_fasta_files = self.get_outputs('{basename_woext}', self.input_fasta)
# Build clusters
cdhit = ShellFunction( self.get_exec_path("cd-hit") + " -i $1 -o $2 -d 0 " + self.cdhit_options + " 2>> " + self.stderr, cmd_format='{EXE} {IN} {OUT}' )
cdhit = ShellFunction( self.get_exec_path("cdhit") + " -i $1 -o $2 -d 0 " + self.cdhit_options + " 2>> " + self.stderr, cmd_format='{EXE} {IN} {OUT}' )
cdhit = MultiMap( cdhit, inputs=self.input_fasta, outputs=[tmp_fasta_files, self.cluster_files] )
# Rename cluster's sequences
......
......@@ -59,7 +59,7 @@ class Framebot (Component):
def process(self):
for idx in range(len(self.input_fasta)):
framebot = ShellFunction( "java -Xmx4g -jar " + self.get_exec_path("FrameBot") + " framebot " + self.options + " -o $1 " + self.bank + " $2 2> $3", cmd_format='{EXE} {ARG} {IN} {OUT}' )
framebot = ShellFunction( "java -Xmx4g -jar " + self.get_exec_path("framebot") + " framebot " + self.options + " -o $1 " + self.bank + " $2 2> $3", cmd_format='{EXE} {ARG} {IN} {OUT}' )
framebot( arguments=self.stem_name[idx],
inputs=self.input_fasta[idx],
outputs=[self.stderr[idx], self.ok_aln[idx], self.discarded_aln[idx], self.corrected_nucleotids[idx], self.failed_nucleotids[idx], self.corrected_proteins[idx]],
......
......@@ -37,5 +37,5 @@ class FramebotIndex (Component):
self.stderr = OutputFile(os.path.join(self.output_directory, "framebotindex.stderr"))
def process(self):
framebotIndex = ShellFunction( "java -Xmx4g -jar " + self.get_exec_path("FrameBot") + " index $1 $2 2> $3", cmd_format='{EXE} {IN} {OUT}' )
framebotIndex = ShellFunction( "java -Xmx4g -jar " + self.get_exec_path("framebot") + " index $1 $2 2> $3", cmd_format='{EXE} {IN} {OUT}' )
framebotIndex(inputs=self.bank, outputs=[self.index, self.stderr])
\ No newline at end of file
Supports Markdown
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment