diff options
Diffstat (limited to 'nixpkgs/pkgs/applications/science/biology/blast/no_slash_bin.patch')
| -rw-r--r-- | nixpkgs/pkgs/applications/science/biology/blast/no_slash_bin.patch | 184 |
1 files changed, 184 insertions, 0 deletions
diff --git a/nixpkgs/pkgs/applications/science/biology/blast/no_slash_bin.patch b/nixpkgs/pkgs/applications/science/biology/blast/no_slash_bin.patch new file mode 100644 index 000000000000..9b78ac579264 --- /dev/null +++ b/nixpkgs/pkgs/applications/science/biology/blast/no_slash_bin.patch @@ -0,0 +1,184 @@ +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 = $(TOUCH) + LN_S = @LN_S@ + GREP = @GREP@ +--- ncbi-blast-2.9.0+-src/src/build-system/configure 2019-03-05 00:49:08.000000000 +0800 ++++ ncbi-blast-2.9.0+-src.patched/src/build-system/configure 2019-05-15 16:55:40.711795042 +0800 +@@ -10417,10 +10417,6 @@ + echo "${ECHO_T}no, using $LN_S" >&6; } + fi + +-case "$LN_S" in +- /*) ;; +- * ) LN_S=/bin/$LN_S ;; +-esac + + if test -n "$ac_tool_prefix"; then + # Extract the first word of "${ac_tool_prefix}ranlib", so it can be a program name with args. |