Mercurial > repos > ucsb-phylogenetics > osiris_phylogenetics
view orthologs/ucsb_hamster/ucsb_galaxy_hamster.sh @ 0:5b9a38ec4a39 draft default tip
First commit of old repositories
author | osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu> |
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date | Tue, 11 Mar 2014 12:19:13 -0700 |
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#!/bin/sh # set -x # Uncomment 'set -x' for debug information ############################################# # UCSB HAMSTER - GALAXY HISTORY # # # # Executed when user chooses Galaxy history # ############################################# # Set your hamster script location here. The directory containing these scripts should be in #your path script="hamstrsearch_local-hmmer3.pl" # Set your unbuild.py script location here unbuild="unbuild.py" # Set your emap2fasta.pl script location here emap2fasta="emap2fasta.pl" # 1 - Sequence input file # 2 - Proteins results output file # 3 - CDS results output file # 4 - Screen log # 5 - Species name # 6 - whether to use EST flag D=DNA so use -est flag P=Protein so do not use -est flag in hmmstr call # 7 - HMM Input from UCSB HMMBUILD # 8 - MUSCLE data from UCSB MUSCLE # 9 - Reference Species File # 10 - Reference Species Name input=$1 proteins=$2 cdsfile=$3 screenlog=$4 speciesName=$5 datatype=$6 hmm_data=$7 muscle_data=$8 filepath=`pwd` tail="_prot" tail2="_temp" # set flag based on input if [ $datatype = "P" ]; then estflag="-protein" else estflag="-est" fi refspfile=${9} refsphist=${10} echo "Protein or EST? : $estflag" >> $screenlog echo "Reference genome file from galaxy history: $refspfile" >> $screenlog echo "Reference species genome name: $refsphist" >> $screenlog # unbuild.py here on $hmm_data mkdir core mkdir core/hmm_dir cp $hmm_data core/core.fa $unbuild core/hmm_dir core/core.fa cp core/hmm_dir/hmmlist.txt core/hmmlist.txt # use formatdb to generate new blastdb from this input file refsphistGALAXY=$refsphist mkdir $refsphistGALAXY cp $muscle_data $refsphistGALAXY/$refsphist$tail2 $emap2fasta $refsphistGALAXY/$refsphist$tail2 $refsphist cp full.fasta core/core.fa cp $refspfile $refsphistGALAXY/$refsphist$tail cd $refsphistGALAXY formatdb -t $refsphist -i $refsphist$tail -n $refsphist$tail echo "*** Direcotry Structure of Ref. Genome ***" >> $screenlog ls -l >> $screenlog echo >> $screenlog cd $filepath # script execution $script -sequence_file=$1 $estflag -taxon=$5 -hmmset=core -refspec=$refsphistGALAXY -galaxyout=$2 -2galaxyout=$cdsfile 2>log.txt >> $screenlog