Revision: 2777 Author: nate Date: 2009-02-18 16:12:38 -0500 (Wed, 18 Feb 2009) Log Message: ----------- Make taxonomy tools compile without changing the source Modified Paths: -------------- dependencies/taxBuilder/tb.readme dependencies/taxonomy2tree/t2t.readme dependencies/taxonomy2tree/taxonomy2tree.c dependencies/tree2PS-fast/t2ps.readme dependencies/tree2PS-fast/tree2ps.c Modified: dependencies/taxBuilder/tb.readme =================================================================== --- dependencies/taxBuilder/tb.readme 2009-02-05 15:19:08 UTC (rev 2776) +++ dependencies/taxBuilder/tb.readme 2009-02-18 21:12:38 UTC (rev 2777) @@ -5,17 +5,9 @@ $gcc -o taxBuilder -fast avl.c main.c On Linux: +$gcc -o taxBuilder -O3 avl.c main.c -Insert the following near the top of main.c - - #define isnumber (c) ( (c>='0') && (c<='9')) - -Replace -fast with -O3 (the letter 'O'): - - $gcc -o taxBuilder -O3 avl.c main.c - INSTALL ======= -Place the binary into a directory that is listed in setup_paths.sh script located in the root of Galaxy installation - +Place the binary into a directory that is in your Galaxy user's $PATH. Modified: dependencies/taxonomy2tree/t2t.readme =================================================================== --- dependencies/taxonomy2tree/t2t.readme 2009-02-05 15:19:08 UTC (rev 2776) +++ dependencies/taxonomy2tree/t2t.readme 2009-02-18 21:12:38 UTC (rev 2777) @@ -5,18 +5,9 @@ $gcc -o taxonomy2tree -fast avl.c taxonomy2tree.c On Linux: +$gcc -o taxonomy2tree -O3 avl.c taxonomy2tree.c -Insert the following near the top of taxonomy2tree.c - - #define isnumber (c) ( (c>='0') && (c<='9')) - -Replace -fast with -O3 (the letter 'O'): - - $gcc -o taxonomy2tree -O3 avl.c taxonomy2tree.c - INSTALL ======= -Place the binary into a directory that is listed in setup_paths.sh script located in the root of Galaxy installation - - +Place the binary into a directory that is in your Galaxy user's $PATH. Modified: dependencies/taxonomy2tree/taxonomy2tree.c =================================================================== --- dependencies/taxonomy2tree/taxonomy2tree.c 2009-02-05 15:19:08 UTC (rev 2776) +++ dependencies/taxonomy2tree/taxonomy2tree.c 2009-02-18 21:12:38 UTC (rev 2777) @@ -7,6 +7,10 @@ #include <time.h> #include <ctype.h> +#ifndef __APPLE__ +#define isnumber (c) ( (c>='0') && (c<='9')) +#endif + #define DEFAULT_STRING_ALLOC 16L #define NUMBER_OF_FIELDS 24 #define NUMBER_OF_TAX_FIELDS 22 Modified: dependencies/tree2PS-fast/t2ps.readme =================================================================== --- dependencies/tree2PS-fast/t2ps.readme 2009-02-05 15:19:08 UTC (rev 2776) +++ dependencies/tree2PS-fast/t2ps.readme 2009-02-18 21:12:38 UTC (rev 2777) @@ -5,18 +5,9 @@ $gcc -o tree2PS-fast -fast avl.c tree2ps.c On Linux: +$gcc -o tree2PS-fast -O3 avl.c tree2ps.c -Insert the following near the top of tree2ps.c - - #define isnumber (c) ( (c>='0') && (c<='9')) - -Replace -fast with -O3 (the letter 'O'): - - $gcc -o tree2PS-fast -O3 avl.c tree2ps.c - INSTALL ======= -Place the binary into a directory that is listed in setup_paths.sh script located in the root of Galaxy installation - - +Place the binary into a directory that is in your Galaxy user's $PATH. Modified: dependencies/tree2PS-fast/tree2ps.c =================================================================== --- dependencies/tree2PS-fast/tree2ps.c 2009-02-05 15:19:08 UTC (rev 2776) +++ dependencies/tree2PS-fast/tree2ps.c 2009-02-18 21:12:38 UTC (rev 2777) @@ -7,6 +7,10 @@ #include <time.h> #include <ctype.h> +#ifndef __APPLE__ +#define isnumber (c) ( (c>='0') && (c<='9')) +#endif + #define DEFAULT_STRING_ALLOC 16L static char *const Usage = "tree2ps newick_file ps_output_file max_tree_level (<=0 to show all levels) font_size (in 2-255, 8 is a good default) \nmax_leaves (<=0 to show all) count_duplicate_tax_id (0 or 1; with 0 multiple copies of the same taxid count as 1)\n";