# HG changeset patch # User iuc # Date 1470076445 14400 # Node ID c4cbfb49f1b66f5ebcef3e47bc0370522c407453 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_mothur_1_36_1 commit e23a8ad798830209db722d5496d19ec7a5e06214 diff -r 000000000000 -r c4cbfb49f1b6 tool_dependencies.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Mon Aug 01 14:34:05 2016 -0400 @@ -0,0 +1,83 @@ + + + + + + https://github.com/mothur/mothur/archive/v1.36.1.zip + + + + + + + + + + + + chmod u+x source/uchime_src/mk + + test $(uname) = Linux && + perl -i.bak -pe 's/(USEREADLINE.+) = yes/$1 = no/; s/TARGET_ARCH \+= -arch x86_64//; s/#(CXXFLAGS.+-mtune=native -march=native -m64)/$1/;' source/makefile || + true + + sed -i.bak -e 's/\ \ \ \ /\t/g' source/makefile; + sed -i.bak -e '141d;151d;152d' source/makefile; + sed -i.bak -e 's/fortranSource//g' source/makefile; + sed -i.bak -e 's/\/usr\/local/${BOOST_ROOT_DIR}\/boost/g' source/makefile; + sed -i.bak -e 's/\${BOOST_LIBRARY_DIR}zlib.a/${ZLIB_ROOT_DIR}\/lib\/libz.a/' source/makefile + + cd source; make -j 2; + + mothur + $INSTALL_DIR/bin + + + source/uchime + $INSTALL_DIR/bin + + + $INSTALL_DIR/bin + + $INSTALL_DIR/bin/blast/bin + $INSTALL_DIR/bin + cd $INSTALL_DIR/bin;mypath=`which blastall`; mypath=`dirname $mypath`; cp $mypath/* ./blast/bin + + + +*Authors & Contacts* +Jim Johnson +Peter Briggs +Iyad Kandalaft | Iyad.Kandalaft@Agr.gc.ca | Agriculture and Agri-Foods Canada +Kevin Chen | Agriculture and Agri-Foods Canada + +*Description* + +The Mothur Tool Suite repository provides Galaxy wrappers for the majority of the Mothur tools. In addition, it downloads and builds the Mothur binaries. + +Supports Linux environments such as Redhat/Centos/Ubuntu as well as Mac OSX. + +These links provide information for building the Mothur package in most environments. + +http://www.mothur.org/wiki/Download_mothur + +http://www.mothur.org/wiki/Installation +http://www.mothur.org/wiki/Makefile_options + +*Requirements* + +- build tools (make, C libraries, GCC) +- libncurses-dev(el) +- simplejson (python library) + + + + + + + + + + + +