Today I installed the latest version of GeneWise, part of Ewan Birney's Wise2.4.1 package (http://www.ebi.ac.uk/~birney/wise2/), on the Sanger compute farm. First I typed the following:% tar -xvf wise2.4.1.tar.gz
% cd wise2.4.1
% cd src
% make all
However, this gave me an error message, and there was no src/bin subdirectory made, so the installation had failed.
After a quick websearch, I found Ian Korf's notes on installing Wise2.4.1 (http://korflab.ucdavis.edu/datasets/cegma/ubuntu_instructions_1.txt), and based on that I did the following:
1) I typed:
% setenv WISECONFIGDIR /nfs/users/nfs_a/alc/Documents/GeneWise/wise2.4.1/wisecfg/
2) I then edited the file src/makefile to change line 25 from 'CC = cc' to 'CC = gcc'.
3) I then edited the file src/dyc/makefile to change line 26 from 'CC = cc' to 'CC = gcc'.
4) I then edited the file src/models/phasemodels.c to change line 23 from 'if( !isnumber(line[0]) ) {' to 'if( !isdigit(line[0]) ) {'
5) I then typed (in the subdirectory src):
% make all
This worked fine, I now have a src/bin subdirectory with executables 'genewise' and 'genewisedb'. Hurray!
1 comment:
I start getting error messages from this point on. I'm using Mac OSX 10.6.8 and Xcode 3.2.6. Any idea how I can sort this out ... I do not see subseqhash.o in dynlibsrc/
if test -x /usr/bin/ranlib; then /usr/bin/ranlib libdyna.a; else exit 0; fi
(cd dynlibsrc ; make CC="gcc" CFLAGS="-c -O3 `glib-config --cflags`" libdyna_glib.a )
/bin/sh: glib-config: command not found
gcc -c -O3 -I../base/ subseqhash.c
In file included from subseqhash.c:4:
subseqhash.h:9:18: error: glib.h: No such file or directory
In file included from subseqhash.c:4:
subseqhash.h:87: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘Wise2_remove_subseq_SeqLookupPos’
subseqhash.dy: In function ‘Wise2_new_ghash_SeqLookupInterface’:
subseqhash.dy:30: error: ‘g_direct_hash’ undeclared (first use in this function)
subseqhash.dy:30: error: (Each undeclared identifier is reported only once
subseqhash.dy:30: error: for each function it appears in.)
subseqhash.dy:30: error: ‘g_direct_equal’ undeclared (first use in this function)
subseqhash.dy:30: warning: cast to pointer from integer of different size
subseqhash.dy: In function ‘Wise2_get_client_subseqhash_ghash’:
subseqhash.dy:46: error: ‘GHashTable’ undeclared (first use in this function)
subseqhash.dy:46: error: ‘t’ undeclared (first use in this function)
subseqhash.dy:46: error: expected expression before ‘)’ token
subseqhash.dy: In function ‘Wise2_free_subseqhash_ghash’:
subseqhash.dy:74: error: ‘GHashTable’ undeclared (first use in this function)
subseqhash.dy:74: error: ‘h’ undeclared (first use in this function)
subseqhash.dy:76: error: expected expression before ‘)’ token
subseqhash.dy:78: error: ‘Wise2_remove_subseq_SeqLookupPos’ undeclared (first use in this function)
subseqhash.dy: At top level:
subseqhash.dy:87: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘Wise2_remove_subseq_SeqLookupPos’
subseqhash.dy: In function ‘Wise2_is_populated_subseqhash_ghash’:
subseqhash.dy:105: error: ‘GHashTable’ undeclared (first use in this function)
subseqhash.dy:105: error: ‘h’ undeclared (first use in this function)
subseqhash.dy:107: error: expected expression before ‘)’ token
subseqhash.dy:111: error: ‘gconstpointer’ undeclared (first use in this function)
subseqhash.dy:111: error: expected ‘)’ before ‘seq_number’
subseqhash.dy:111: warning: comparison between pointer and integer
subseqhash.dy: In function ‘Wise2_lookup_subseqhash_ghash’:
subseqhash.dy:124: error: ‘GHashTable’ undeclared (first use in this function)
subseqhash.dy:124: error: ‘h’ undeclared (first use in this function)
subseqhash.dy:126: error: expected expression before ‘)’ token
make[1]: *** [subseqhash.o] Error 1
make: *** [realall] Error 2
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