{"id":844,"date":"2022-06-23T04:24:39","date_gmt":"2022-06-22T20:24:39","guid":{"rendered":"http:\/\/www.wuchangsong.com\/?p=844"},"modified":"2022-06-23T04:25:14","modified_gmt":"2022-06-22T20:25:14","slug":"popcogent%e5%ae%89%e8%a3%85%e5%8f%8a%e4%bd%bf%e7%94%a8","status":"publish","type":"post","link":"http:\/\/www.wuchangsong.com\/?p=844","title":{"rendered":"PopCOGenT\u5b89\u88c5\u53ca\u4f7f\u7528"},"content":{"rendered":"<p>\u4ecePopCOGenT github\u4e0b\u8f7dPopCOGenT.yml\u540e\u4f7f\u7528conda\u5b89\u88c5\u8f6f\u4ef6\u8fd0\u884c\u9700\u8981\u73af\u5883<\/p>\n<pre>conda config --set restore_free_channel true\nconda env create -f PopCOGenT.yml\nconda activate PopCOGenT\n##\u4e0b\u8f7dmugsy\u5e76\u89e3\u538b\nexport MUGSY_INSTALL=\/path\/to\/install\/mugsy\npython get_alignment_and_length_bias.py --genome_dir \/home\/wuchangsong\/Streptococcus_agalactiae\/test\/ --genome_ext .fasta --alignment_dir .\/output --mugsy_path \/opt\/biosoft\/PopCOGenT\/mugsy_x86-64-v1r2.3\/mugsy --mugsy_env \/opt\/biosoft\/PopCOGenT\/mugsy_x86-64-v1r2.3\/mugsyenv.sh --base_name test_12 --num_threads 150\n##\u5b89\u88c5infomap\ngit clone https:\/\/github.com\/mapequation\/infomap.git\ncd infomap\nmake\n##gcc\u8981\u6c424.9\u4ee5\u4e0a\uff0c\u4e0d\u7136\u62a5\u9519\uff08g++: error: unrecognized command line option \u2018-std=c++14\u2019\uff09\n##\u5b89\u88c5gcc-11.2.0\uff08root\u7528\u6237\uff09\nwget http:\/\/ftp.gnu.org\/gnu\/gcc\/gcc-11.2.0\/gcc-11.2.0.tar.gz\ntar -zxvf gcc-11.2.0.tar.gz\ncd gcc-11.2.0\n.\/contrib\/download_prerequisites\nmkdir build\ncd build\/\n..\/configure -enable-checking=release -enable-languages=c,c++ -disable-multilib\nmake -j 160\nmake install\n##\u91cd\u65b0\u6253\u5f00\u7ec8\u7aefgcc -v\n##\u5b89\u88c5gcc-11.2.0\u540einfomap make\u6210\u529f\uff0c\u7136\u800c.\/Infomap\u62a5\u9519\n##.\/Infomap: \/lib64\/libstdc++.so.6: version `GLIBCXX_3.4.20' not found (required by .\/Infomap)\n##.\/Infomap: \/lib64\/libstdc++.so.6: version `CXXABI_1.3.9' not found (required by .\/Infomap)\n##.\/Infomap: \/lib64\/libstdc++.so.6: version `GLIBCXX_3.4.29' not found (required by .\/Infomap)\nstrings \/usr\/lib64\/libstdc++.so.6 | grep GLIBCXX_##\u53d1\u73b0\u786e\u5b9e\u5c11\u4e86\u5e93\u6587\u4ef6\ncp \/usr\/local\/lib64\/libstdc++.so.6.0.29 \/usr\/lib64\/\ncd \/usr\/lib64\/ &amp;&amp; rm libstdc++.so.6\nln -s libstdc++.so.6.0.29 .\/libstdc++.so.6\n##\u8fdb\u5165infomap\u5b89\u88c5\u76ee\u5f55\n.\/Infomap -h\n##Infomap\u6ca1\u6709\u62a5\u9519\u53ef\u4ee5\u8fd0\u884ccluster.py\uff0cinfomap\u5b89\u88c5\u6700\u65b0\u7248\u672c\u8fd0\u884c\u65f6\u9700\u8981\u5c06cluster.py\u7684\u7b2c107\u884c-i\u6539\u4e3a-c\uff0c\u56e0\u4e3av2.5.0\u8f93\u5165\u53c2\u6570\u4e3a-c\uff0c\u4f5c\u8005\u63a8\u8350\u7684v0.18.3\u8f93\u5165\u53c2\u6570\u4e3a-i\u3002infomap github\u5df2\u627e\u4e0d\u5230v0.18.3\uff0c\u5982\u679c\u4e0d\u60f3\u9ebb\u70e6\u4e0b\u8f7d\u6700\u65b0\u7248\u672c\u7684infomap\uff0c\u53ef\u4ee5\u8fdb\u5165PopCOGenT\u7684\u5b89\u88c5\u76ee\u5f55\uff0c\u5728Infomap\u76ee\u5f55\u4e0bmake\u5373\u53ef\uff0c\u8fd9\u662f\u4f5c\u8005\u63d0\u4f9b\u7684v0.18.3\u3002\npython cluster.py --base_name test_12 --length_bias_file test_12.length_bias.txt --output_directory output --infomap_path \/opt\/biosoft\/PopCOGenT-master\/Infomap\/Infomap --single_cell\n\n<\/pre>\n","protected":false},"excerpt":{"rendered":"<p>\u4ecePopCOGenT github\u4e0b\u8f7dPopCOGenT.yml\u540e\u4f7f\u7528conda\u5b89\u88c5\u8f6f\u4ef6\u8fd0\u884c\u9700\u8981\u73af\u5883 conda config &#8211;set restore_free_channel true conda env create -f PopCOGenT.yml conda activate PopCOGenT ##\u4e0b\u8f7dmugsy\u5e76\u89e3\u538b export MUGSY_INSTALL=\/path\/to\/install\/mugsy python get_alignment_and_length_bias.py &#8211;genome_dir \/home\/wuchangsong\/Streptococcus_agalactiae\/test\/ &#8211;genome_ext .fasta &#8211;alignment_dir .\/output &#8211;mugsy_path \/opt\/biosoft\/PopCOGenT\/mugsy_x86-64-v1r2.3\/mugsy &#8211;mugsy_env \/opt\/biosoft\/PopCOGenT\/mugsy_x86-64-v1r2.3\/mugsyenv.sh &#8211;base_name test_12 &#8211;num_threads 150 ##\u5b89\u88c5infomap git clone https:\/\/github.com\/mapequation\/infomap.git cd infomap make ##gcc\u8981\u6c424.9\u4ee5\u4e0a\uff0c\u4e0d\u7136\u62a5\u9519\uff08g++: error: unrecognized command line option \u2018-std=c++14\u2019\uff09 ##\u5b89\u88c5gcc-11.2.0\uff08root\u7528\u6237\uff09 wget http:\/\/ftp.gnu.org\/gnu\/gcc\/gcc-11.2.0\/gcc-11.2.0.tar.gz tar -zxvf gcc-11.2.0.tar.gz cd [&hellip;]<\/p>\n","protected":false},"author":1,"featured_media":0,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"footnotes":""},"categories":[4,3,2],"tags":[],"_links":{"self":[{"href":"http:\/\/www.wuchangsong.com\/index.php?rest_route=\/wp\/v2\/posts\/844"}],"collection":[{"href":"http:\/\/www.wuchangsong.com\/index.php?rest_route=\/wp\/v2\/posts"}],"about":[{"href":"http:\/\/www.wuchangsong.com\/index.php?rest_route=\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"http:\/\/www.wuchangsong.com\/index.php?rest_route=\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"http:\/\/www.wuchangsong.com\/index.php?rest_route=%2Fwp%2Fv2%2Fcomments&post=844"}],"version-history":[{"count":7,"href":"http:\/\/www.wuchangsong.com\/index.php?rest_route=\/wp\/v2\/posts\/844\/revisions"}],"predecessor-version":[{"id":853,"href":"http:\/\/www.wuchangsong.com\/index.php?rest_route=\/wp\/v2\/posts\/844\/revisions\/853"}],"wp:attachment":[{"href":"http:\/\/www.wuchangsong.com\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=844"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"http:\/\/www.wuchangsong.com\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=844"},{"taxonomy":"post_tag","embeddable":true,"href":"http:\/\/www.wuchangsong.com\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=844"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}