nixpkgs-suyu/pkgs/applications/science/biology/blast/no_slash_bin.patch

diff -u --recursive ncbi-blast-2.9.0+-src/scripts/common/impl/collect_outside_libs.sh ncbi-blast-2.9.0+-src.patched/scripts/common/impl/collect_outside_libs.sh
--- ncbi-blast-2.9.0+-src/scripts/common/impl/collect_outside_libs.sh	2014-08-01 22:01:17.000000000 +0800
+++ ncbi-blast-2.9.0+-src.patched/scripts/common/impl/collect_outside_libs.sh	2019-05-15 12:40:44.145239480 +0800
@@ -1,8 +1,5 @@
 #!/bin/sh
 set -e
-PATH=/bin:/usr/bin
-export PATH
-unset CDPATH
 
 base=$1
 search=`echo ${2-$LD_LIBRARY_PATH} | tr : ' '`
diff -u --recursive ncbi-blast-2.9.0+-src/scripts/common/impl/create_flat_tuneups.sh ncbi-blast-2.9.0+-src.patched/scripts/common/impl/create_flat_tuneups.sh
--- ncbi-blast-2.9.0+-src/scripts/common/impl/create_flat_tuneups.sh	2011-08-17 02:55:10.000000000 +0800
+++ ncbi-blast-2.9.0+-src.patched/scripts/common/impl/create_flat_tuneups.sh	2019-05-15 12:40:48.449276574 +0800
@@ -1,9 +1,6 @@
 #!/bin/sh
 id='$Id: create_flat_tuneups.sh 331412 2011-08-16 18:55:10Z ucko $'
 
-PATH=/bin:/usr/bin
-export PATH
-
 exec > auto_flat_tuneups.mk
 
 cat <<EOF
diff -u --recursive ncbi-blast-2.9.0+-src/scripts/common/impl/get_lock.sh ncbi-blast-2.9.0+-src.patched/scripts/common/impl/get_lock.sh
--- ncbi-blast-2.9.0+-src/scripts/common/impl/get_lock.sh	2011-08-20 04:12:28.000000000 +0800
+++ ncbi-blast-2.9.0+-src.patched/scripts/common/impl/get_lock.sh	2019-05-15 12:40:52.901315000 +0800
@@ -1,7 +1,5 @@
 #!/bin/sh
 
-PATH=/bin:/usr/bin
-export PATH
 
 dir=$1.lock
 
diff -u --recursive ncbi-blast-2.9.0+-src/scripts/common/impl/if_diff.sh ncbi-blast-2.9.0+-src.patched/scripts/common/impl/if_diff.sh
--- ncbi-blast-2.9.0+-src/scripts/common/impl/if_diff.sh	2014-07-30 22:06:45.000000000 +0800
+++ ncbi-blast-2.9.0+-src.patched/scripts/common/impl/if_diff.sh	2019-05-15 12:42:57.298410841 +0800
@@ -4,9 +4,6 @@
 # Author:  Denis Vakatov (vakatov@ncbi.nlm.nih.gov)
 #################################
 
-orig_PATH=$PATH
-PATH=/bin:/usr/bin
-
 script_name=`basename $0`
 script_args="$*"
 
@@ -16,7 +13,7 @@
 base_action=`basename "$action"`
 case "$base_action" in
   cp | cp\ * | ln | ln\ * )
-      action=/bin/$base_action
+      action=$base_action
       rm="rm -f"
       ;;
   * )
@@ -58,10 +55,8 @@
   shift
   cmd="$* $dest_file"
   test "$quiet" = yes || echo "$cmd"
-  PATH=$orig_PATH
   "$@" "$dest"
   status=$?
-  PATH=/bin:/usr/bin
   return $status
 }
 
@@ -74,7 +69,7 @@
   case "$base_action" in
     ln | ln\ -f )
       test "$quiet" = yes || echo "failed; trying \"cp -p ...\" instead"
-      cmd="/bin/cp -p $src_file $dest_file"
+      cmd="cp -p $src_file $dest_file"
       ExecHelper "$dest_file" /bin/cp -p "$src_file"  ||
       Usage "\"$cmd\" failed"
       ;;
diff -u --recursive ncbi-blast-2.9.0+-src/scripts/common/impl/make_lock_map.sh ncbi-blast-2.9.0+-src.patched/scripts/common/impl/make_lock_map.sh
--- ncbi-blast-2.9.0+-src/scripts/common/impl/make_lock_map.sh	2011-11-17 04:43:52.000000000 +0800
+++ ncbi-blast-2.9.0+-src.patched/scripts/common/impl/make_lock_map.sh	2019-05-15 12:40:56.769348434 +0800
@@ -1,8 +1,6 @@
 #!/bin/sh
 # $Id: make_lock_map.sh 344587 2011-11-16 20:43:52Z ucko $
 
-PATH=/bin:/usr/bin
-export PATH
 
 act=false
 cache_dir='.#SRC-cache'
diff -u --recursive ncbi-blast-2.9.0+-src/scripts/common/impl/run_with_lock.sh ncbi-blast-2.9.0+-src.patched/scripts/common/impl/run_with_lock.sh
--- ncbi-blast-2.9.0+-src/scripts/common/impl/run_with_lock.sh	2015-10-29 22:36:05.000000000 +0800
+++ ncbi-blast-2.9.0+-src.patched/scripts/common/impl/run_with_lock.sh	2019-05-15 12:41:53.401842849 +0800
@@ -1,10 +1,6 @@
 #!/bin/sh
 # $Id: run_with_lock.sh 483249 2015-10-29 14:36:05Z ucko $
 
-orig_PATH=$PATH
-PATH=/bin:/usr/bin
-export PATH
-
 base=
 logfile=
 map=
@@ -23,7 +19,7 @@
 : ${base:=`basename "$1"`}
 
 clean_up () {
-    /bin/rm -rf "$base.lock"
+    rm -rf "$base.lock"
 }
 
 case $0 in
@@ -45,7 +41,7 @@
     trap "clean_up; exit $error_status" 1 2 15
     if [ -n "$logfile" ]; then
         status_file=$base.lock/status
-        (PATH=$orig_PATH; export PATH; "$@"; echo $? > "$status_file") 2>&1 \
+        ("$@"; echo $? > "$status_file") 2>&1 \
             | tee "$logfile.new"
         # Emulate egrep -q to avoid having to move from under scripts.
         if [ ! -f "$logfile" ]  \
@@ -58,8 +54,6 @@
             status=1
         fi
     else
-        PATH=$orig_PATH
-        export PATH
         "$@"
         status=$?
     fi
diff -u --recursive ncbi-blast-2.9.0+-src/scripts/common/impl/strip_for_install.sh ncbi-blast-2.9.0+-src.patched/scripts/common/impl/strip_for_install.sh
--- ncbi-blast-2.9.0+-src/scripts/common/impl/strip_for_install.sh	2013-09-24 03:06:51.000000000 +0800
+++ ncbi-blast-2.9.0+-src.patched/scripts/common/impl/strip_for_install.sh	2019-05-15 12:40:13.272975092 +0800
@@ -1,8 +1,5 @@
 #!/bin/sh
 
-PATH=/bin:/usr/bin:/usr/ccs/bin
-export PATH
-
 case "$1" in
     --dirs )
         shift
--- ncbi-blast-2.9.0+-src/scripts/common/impl/update_configurable.sh	2017-07-13 22:53:24.000000000 +0800
+++ ncbi-blast-2.9.0+-src.patched/scripts/common/impl/update_configurable.sh	2019-05-15 15:03:35.861276083 +0800
@@ -1,6 +1,4 @@
 #!/bin/sh
-PATH=/bin:/usr/bin
-export PATH
 
 script_name=`basename $0`
 script_dir=`dirname $0`
--- ncbi-blast-2.9.0+-src/src/build-system/Makefile.mk.in	2019-01-04 01:38:37.000000000 +0800
+++ ncbi-blast-2.9.0+-src.patched/src/build-system/Makefile.mk.in	2019-05-15 15:14:41.749416495 +0800
@@ -50,12 +50,12 @@
 
 ### Auxiliary commands, filters
 
-RM       = /bin/rm -f
-RMDIR    = /bin/rm -rf
-COPY     = /bin/cp -p
+RM       = rm -f
+RMDIR    = rm -rf
+COPY     = cp -p
 BINCOPY  = @BINCOPY@
 TOUCH    = @TOUCH@
-MKDIR    = /bin/mkdir
+MKDIR    = mkdir
 BINTOUCH = $(TOUCH)
 LN_S     = @LN_S@
 GREP     = @GREP@
--- ncbi-blast-2.9.0+-src/src/build-system/configure	2019-03-05 00:49:08.000000000 +0800
+++ ncbi-blast-2.9.0+-src.patched/src/build-system/configure	2019-05-15 16:55:40.711795042 +0800
@@ -10417,4 +10417,0 @@
-case "$LN_S" in
-    /*) ;;
-    * ) LN_S=/bin/$LN_S ;;
-esac