Loading LICENSE +43 −25 Original line number Diff line number Diff line Copyright (c) 2014, MarBL All rights reserved. PURPOSE Parsnp is a command-line-tool for efficient microbial core genome alignment and SNP detection. Parsnp was designed to work in tandem with Gingr, a flexible platform for visualizing genome alignments and phylogenetic trees; both Parsnp and Gingr form part of the Harvest suite. Parsnp is implemented in C++ and Python. COPYRIGHT LICENSE Copyright © 2014, Battelle National Biodefense Institute (BNBI); all rights reserved. Authored by: Brian Ondov, Todd Treangen, and Adam Phillippy This Software was prepared for the Department of Homeland Security (DHS) by the Battelle National Biodefense Institute, LLC (BNBI) as part of contract HSHQDC-07-C-00020 to manage and operate the National Biodefense Analysis and Countermeasures Center (NBACC), a Federally Funded Research and Development Center. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. 1. Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. 2. Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the {organization} nor the names of its 3. Neither the name of the copyright holder nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. Parsnp.py +125 −120 File changed.Preview size limit exceeded, changes collapsed. Show changes build_parsnp_linux.sh +2 −0 Original line number Diff line number Diff line Loading @@ -5,4 +5,6 @@ make install cd .. ./autogen.sh ./configure echo "Fix MUSCLE-3.7 linker" make LDADD=-lMUSCLE-3.7 make install build_parsnp_osx.sh +2 −0 Original line number Diff line number Diff line Loading @@ -7,4 +7,6 @@ make install cd .. ./autogen.sh ./configure echo "Fix MUSCLE-3.7 linker" make LDADD=-lMUSCLE-3.7 make install install.py +4 −4 Original line number Diff line number Diff line import os,sys,string #parsnp basic INSTALL script user_home = os.environ["HOME"] print "<<Welcome to Parsnp utility script install>>" print("<<Welcome to Parsnp utility script install>>") #check for python version if (sys.version_info[0] < 2) or (sys.version_info[0] == 2 and sys.version_info[1] < 6): if (sys.version_info[0] < 3) or (sys.version_info[0] == 3 and sys.version_info[1] < 1): print "Python version is %s. Parsnp requires at least 2.6"%(sys.version) print("Python version is %s. Parsnp requires at least 3.1"%(sys.version)) sys.exit(1) #complete shebang Loading Loading
LICENSE +43 −25 Original line number Diff line number Diff line Copyright (c) 2014, MarBL All rights reserved. PURPOSE Parsnp is a command-line-tool for efficient microbial core genome alignment and SNP detection. Parsnp was designed to work in tandem with Gingr, a flexible platform for visualizing genome alignments and phylogenetic trees; both Parsnp and Gingr form part of the Harvest suite. Parsnp is implemented in C++ and Python. COPYRIGHT LICENSE Copyright © 2014, Battelle National Biodefense Institute (BNBI); all rights reserved. Authored by: Brian Ondov, Todd Treangen, and Adam Phillippy This Software was prepared for the Department of Homeland Security (DHS) by the Battelle National Biodefense Institute, LLC (BNBI) as part of contract HSHQDC-07-C-00020 to manage and operate the National Biodefense Analysis and Countermeasures Center (NBACC), a Federally Funded Research and Development Center. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. 1. Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. 2. Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the {organization} nor the names of its 3. Neither the name of the copyright holder nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
build_parsnp_linux.sh +2 −0 Original line number Diff line number Diff line Loading @@ -5,4 +5,6 @@ make install cd .. ./autogen.sh ./configure echo "Fix MUSCLE-3.7 linker" make LDADD=-lMUSCLE-3.7 make install
build_parsnp_osx.sh +2 −0 Original line number Diff line number Diff line Loading @@ -7,4 +7,6 @@ make install cd .. ./autogen.sh ./configure echo "Fix MUSCLE-3.7 linker" make LDADD=-lMUSCLE-3.7 make install
install.py +4 −4 Original line number Diff line number Diff line import os,sys,string #parsnp basic INSTALL script user_home = os.environ["HOME"] print "<<Welcome to Parsnp utility script install>>" print("<<Welcome to Parsnp utility script install>>") #check for python version if (sys.version_info[0] < 2) or (sys.version_info[0] == 2 and sys.version_info[1] < 6): if (sys.version_info[0] < 3) or (sys.version_info[0] == 3 and sys.version_info[1] < 1): print "Python version is %s. Parsnp requires at least 2.6"%(sys.version) print("Python version is %s. Parsnp requires at least 3.1"%(sys.version)) sys.exit(1) #complete shebang Loading
