4 files changed, 72 insertions, 0 deletions

diff --git a/biology/consed/files/patch-misc_mktrace.c b/biology/consed/files/patch-misc_mktrace.c
new file mode 100644
index 000000000000..99fa065b0bbf
--- /dev/null
+++ b/biology/consed/files/patch-misc_mktrace.c
@@ -0,0 +1,14 @@
+--- misc/mktrace/mktrace.c.orig	Tue Aug 31 03:14:17 2004
++++ misc/mktrace/mktrace.c	Wed Jul 13 16:31:28 2005
+@@ -70,9 +70,9 @@
+   else
+   {
+     printf( "enter FASTA filename: " );
+-    gets( ifnm );
++    fgets( ifnm, sizeof(ifnm), stdin );
+     printf( "enter output filename: " );
+-    gets( ofnm );
++    fgets( ofnm, sizeof(ofnm), stdin );
+   }
+ 
+   /*
diff --git a/biology/consed/files/patch-scripts_addReads2Consed.perl b/biology/consed/files/patch-scripts_addReads2Consed.perl
new file mode 100644
index 000000000000..094a7028a701
--- /dev/null
+++ b/biology/consed/files/patch-scripts_addReads2Consed.perl
@@ -0,0 +1,11 @@
+--- scripts/addReads2Consed.perl.orig	2007-09-26 04:02:19.000000000 +0900
++++ scripts/addReads2Consed.perl	2007-12-11 17:27:20.000000000 +0900
+@@ -71,7 +71,7 @@
+ $szVectorFile = $szConsedHome . "/lib/screenLibs/vector.seq";
+ 
+ # change this to reflect wherever you put the phred parameter file
+-$szPhredParameterFile = $szConsedHome . "/lib/phredpar.dat";
++$szPhredParameterFile = $szConsedHome . "/etc/PhredPar/phredpar.dat";
+ #$szPhredParameterFile = "/usr/local/common/lib/PhredPar/phredpar.dat";
+ #$szPhredParameterFile = "/usr/local/etc/PhredPar/phredpar.dat";
+ 
diff --git a/biology/consed/files/patch-scripts_determineReadTypes.perl b/biology/consed/files/patch-scripts_determineReadTypes.perl
new file mode 100644
index 000000000000..70405b43cca2
--- /dev/null
+++ b/biology/consed/files/patch-scripts_determineReadTypes.perl
@@ -0,0 +1,11 @@
+--- scripts/determineReadTypes.perl.orig	Tue Aug 31 03:14:13 2004
++++ scripts/determineReadTypes.perl	Wed Jul 13 17:00:22 2005
+@@ -177,7 +177,7 @@
+ # you can remove or comment out this line when you are satisfied with
+ # your customized version of this file.
+ 
+-die "You must edit determineReadTypes.perl--please read README.txt that came with consed.  Look under INSTALLING CONSED.  Also look at the comments at the beginning of determineReadTypes.perl  Then, and only then, comment out the line in determineReadTypes.perl that begins with \"die\" and has this error message\n by putting a # in front of that line";
++#die "You must edit determineReadTypes.perl--please read README.txt that came with consed.  Look under INSTALLING CONSED.  Also look at the comments at the beginning of determineReadTypes.perl  Then, and only then, comment out the line in determineReadTypes.perl that begins with \"die\" and has this error message\n by putting a # in front of that line";
+ 
+ $szVersion = "001205";
+ 
diff --git a/biology/consed/files/patch-scripts_phredPhrap b/biology/consed/files/patch-scripts_phredPhrap
new file mode 100644
index 000000000000..5ac28e3d808a
--- /dev/null
+++ b/biology/consed/files/patch-scripts_phredPhrap
@@ -0,0 +1,36 @@
+--- scripts/phredPhrap.orig	2007-09-26 04:02:20.000000000 +0900
++++ scripts/phredPhrap	2007-12-11 17:32:27.000000000 +0900
+@@ -101,7 +101,7 @@
+ 
+ 
+ # change this to reflect wherever you put the phredpar.dat file
+-$szPhredParameterFile = $szConsedHome . "/lib/phredpar.dat";
++$szPhredParameterFile = $szConsedHome . "/etc/PhredPar/phredpar.dat";
+ #$szPhredParameterFile = "/usr/local/common/lib/PhredPar/phredpar.dat";
+ #$szPhredParameterFile = "/usr/local/etc/PhredPar/phredpar.dat";
+ 
+@@ -207,7 +207,7 @@
+ $chromatDirPath = "../chromat_dir";
+ $phdDirPath = "../phd_dir";
+ 
+-$niceExe = "/bin/nice";
++$niceExe = "/usr/bin/nice";
+ $mvExe = "/bin/mv";
+ $lsExe = "/bin/ls";
+ $pwdExe = "/bin/pwd";
+@@ -568,11 +568,11 @@
+ 
+ # only uncomment the following 4 lines when you have customized 
+ # determineReadTypes.perl
+-#print "\n\n--------------------------------------------------------\n";
+-#print "Now running determineReadTypes.perl...\n";
+-#print "--------------------------------------------------------\n\n\n";
++print "\n\n--------------------------------------------------------\n";
++print "Now running determineReadTypes.perl...\n";
++print "--------------------------------------------------------\n\n\n";
+ 
+-#!system( "$determineReadTypes" ) || die "some problem running determineReadTypes.perl $!\n";
++!system( "$determineReadTypes" ) || die "some problem running determineReadTypes.perl $!\n";
+ 
+ 
+ print "\n\n--------------------------------------------------------\n";