Mercurial > repos > rliterman > csp2
annotate CSP2/CSP2_env/env-d9b9114564458d9d-741b3de822f2aaca6c6caa4325c4afce/opt/mummer-3.23/conda_build.sh @ 69:33d812a61356
planemo upload commit 2e9511a184a1ca667c7be0c6321a36dc4e3d116d
| author | jpayne |
|---|---|
| date | Tue, 18 Mar 2025 17:55:14 -0400 |
| parents | |
| children |
| rev | line source |
|---|---|
| jpayne@69 | 1 if [ -z ${CONDA_BUILD+x} ]; then |
| jpayne@69 | 2 source /opt/conda/conda-bld/mummer_1734020773944/work/build_env_setup.sh |
| jpayne@69 | 3 fi |
| jpayne@69 | 4 #!/bin/bash |
| jpayne@69 | 5 |
| jpayne@69 | 6 set -xe |
| jpayne@69 | 7 |
| jpayne@69 | 8 BINARY=mummer |
| jpayne@69 | 9 BINARY_HOME=$PREFIX/bin |
| jpayne@69 | 10 MUMMER_HOME=$PREFIX/opt/mummer-$PKG_VERSION |
| jpayne@69 | 11 |
| jpayne@69 | 12 mkdir -p $BINARY_HOME |
| jpayne@69 | 13 mkdir -p $MUMMER_HOME |
| jpayne@69 | 14 |
| jpayne@69 | 15 # cd to location of Makefile and source |
| jpayne@69 | 16 cp -R $SRC_DIR/* $MUMMER_HOME |
| jpayne@69 | 17 |
| jpayne@69 | 18 cd $MUMMER_HOME |
| jpayne@69 | 19 |
| jpayne@69 | 20 # One of the Makefiles references a shell script not in the path |
| jpayne@69 | 21 export PATH="$PATH:." |
| jpayne@69 | 22 make CC=$CC CXX=$CXX CPPFLAGS="-O3 -DSIXTYFOURBITS" |
| jpayne@69 | 23 |
| jpayne@69 | 24 binaries="\ |
| jpayne@69 | 25 combineMUMs \ |
| jpayne@69 | 26 delta-filter \ |
| jpayne@69 | 27 dnadiff \ |
| jpayne@69 | 28 exact-tandems \ |
| jpayne@69 | 29 mapview \ |
| jpayne@69 | 30 mgaps \ |
| jpayne@69 | 31 mummer \ |
| jpayne@69 | 32 mummerplot \ |
| jpayne@69 | 33 nucmer \ |
| jpayne@69 | 34 promer \ |
| jpayne@69 | 35 repeat-match \ |
| jpayne@69 | 36 run-mummer1 \ |
| jpayne@69 | 37 run-mummer3 \ |
| jpayne@69 | 38 show-aligns \ |
| jpayne@69 | 39 show-coords \ |
| jpayne@69 | 40 show-diff \ |
| jpayne@69 | 41 show-snps \ |
| jpayne@69 | 42 show-tiling \ |
| jpayne@69 | 43 " |
| jpayne@69 | 44 |
| jpayne@69 | 45 # patch defined(%hash) out |
| jpayne@69 | 46 # https://github.com/bioconda/bioconda-recipes/issues/1254 |
| jpayne@69 | 47 |
| jpayne@69 | 48 perl -i -pe 's/defined \(%/\(%/' mummerplot |
| jpayne@69 | 49 |
| jpayne@69 | 50 #Fix escaping symbol @ included in the path to the library (mainly for conda virtual env with galaxy) |
| jpayne@69 | 51 for i in exact-tandems dnadiff mapview mummerplot nucmer promer run-mummer1 run-mummer3; do |
| jpayne@69 | 52 perl -i -pe 's/(envs\/\_\_.*)(\K\@)/\\@/' $i |
| jpayne@69 | 53 done |
| jpayne@69 | 54 |
| jpayne@69 | 55 # fix hashbang lines to use conda's perl |
| jpayne@69 | 56 for i in dnadiff mapview mummerplot nucmer promer; do |
| jpayne@69 | 57 sed -i.bak '1 s|^#!/.*/perl -w$|#!/usr/bin/env perl|g' $MUMMER_HOME/$i |
| jpayne@69 | 58 rm -rf $MUMMER_HOME/$i.bak |
| jpayne@69 | 59 done |
| jpayne@69 | 60 |
| jpayne@69 | 61 for i in $binaries; do |
| jpayne@69 | 62 # ensure executable and setup symlink for binary |
| jpayne@69 | 63 chmod +x $MUMMER_HOME/$i |
| jpayne@69 | 64 ln -s "$MUMMER_HOME/$i" "$BINARY_HOME/$i" |
| jpayne@69 | 65 done |
| jpayne@69 | 66 |
| jpayne@69 | 67 # clean up |
| jpayne@69 | 68 find $MUMMER_HOME -name *.o -exec rm -f {} \; |