#!/bin/sh # A short test for mrbump. Requires that clustalw and fasta be installed. # The first test does not require internet connectivity. # Test first for the clustalw and fasta executables in the PATH clustalw_found=False mafft_found=False fasta_found=False PATH_list=`echo $PATH | sed s'|:| |'g | xargs` # Look for new location of clustalw2 and mafft if test -x $CCP4/libexec/clustalw2; then clustalw_found=True; fi; if test -x $CCP4/libexec/mafft; then mafft_found=True; fi; # Look for clustalw for i in $PATH_list; do if test -x $i/clustalw; then clustalw_found=True; fi; done for i in $PATH_list; do if test -x $i/clustalw2; then clustalw_found=True; fi; done # Look for fasta for i in $PATH_list; do if test -x $i/fasta34; then fasta_found=True; fi; done for i in $PATH_list; do if test -x $i/fasta35; then fasta_found=True; fi; done for i in $PATH_list; do if test -x $i/fasta36; then fasta_found=True; fi; done # If both are missing if [ ${fasta_found} = False ] && [ ${clustalw_found} = False ] then echo "Error: Clustalw executable not found. MrBUMP requires the alignment" 1>&2 echo " program Clustalw be installed in order to run this test." 1>&2 echo "" 1>&2 echo "Error: Fasta executable not found. MrBUMP requires the Fasta" 1>&2 echo " program (fasta34 or fasta35 or fasta36) be installed in order to" 1>&2 echo " run this test." 1>&2 echo "" 1>&2 exit fi # If clustalw is missing if [ $clustalw_found = False ] then echo "Error: Clustalw executable not found. MrBUMP requires the alignment" 1>&2 echo " program Clustalw be installed in order to run this test." 1>&2 echo "" 1>&2 exit else echo "Clustalw executable found in PATH." echo "" fi # If fasta is missing if [ $fasta_found = False ] then echo "Error: Fasta executable not found. MrBUMP requires the Fasta" 1>&2 echo " program (fasta34 or fasta35 or fasta36) be installed in order to" 1>&2 echo " run this test." 1>&2 echo "" 1>&2 exit else echo "Fasta executable found in PATH." echo "" fi # Remove any files left over from a previous run of this test rm -rf $CCP4_SCR/mrbump_test_temp.mtz $CCP4_SCR/mrbump_test_temp.pdb $CCP4_SCR/search_test_mrbump # Run the simple test (Toxd example) mrbump HKLIN $CEXAM/toxd/toxd.mtz SEQIN $CEXAM/toxd/toxd.seq HKLOUT $CCP4_SCR/mrbump_test_temp.mtz XYZOUT $CCP4_SCR/mrbump_test_temp.pdb <