{"id":5317,"date":"2024-09-20T10:01:03","date_gmt":"2024-09-20T02:01:03","guid":{"rendered":""},"modified":"2024-09-20T10:01:03","modified_gmt":"2024-09-20T02:01:03","slug":"reaper\u8f6f\u4ef6\u5b89\u88c5_CurseForge\u6574\u5408\u5305\u5b89\u88c5","status":"publish","type":"post","link":"https:\/\/mushiming.com\/5317.html","title":{"rendered":"reaper\u8f6f\u4ef6\u5b89\u88c5_CurseForge\u6574\u5408\u5305\u5b89\u88c5"},"content":{"rendered":"<p><svg xmlns=\"http:\/\/www.w3.org\/2000\/svg\" style=\"display: none;\"> \n <path stroke-linecap=\"round\" d=\"M5,0 0,2.5 5,5z\" id=\"raphael-marker-block\" style=\"-webkit-tap-highlight-color: rgba(0, 0, 0, 0);\"><\/path> \n<\/svg> <\/p>\n<h2>RepeatModeler\u7684\u5b89\u88c5\uff08\u5305\u542bRepeatMasker\u5b89\u88c5\uff09<\/h2>\n<p>nym 2021-8-15<\/p>\n<h3>\u4e00\u3001RepeatMasker\u5b98\u7f51\u5730\u5740\uff08http:\/\/www.repeatmasker.org\/\uff09<\/h3>\n<h5>\u5b89\u88c5RepeatMasker\u9700\u8981TRF\u3001rmblast<\/h5>\n<h5>1\u3001TRF\u7684\u5b89\u88c5<\/h5>\n<pre class=\"language-java prettyprint linenums\"><code>#\u4e0b\u8f7d\uff08https:\/\/github.com\/Benson-Genomics-Lab\/TRF\uff09 git clone https:\/\/github.com\/Benson-Genomics-Lab\/TRF.git #Check actual version #tar -xzvf trf-4.10.0.tar.gz cd TRF mkdir build cd build ..\/configure make #To install to system sudo make install <\/code><\/pre>\n<h5>2\u3001rmblast\u7684\u5b89\u88c5<\/h5>\n<pre class=\"language-java prettyprint linenums\"><code>#\u4e0b\u8f7d\uff08http:\/\/www.repeatmasker.org\/rmblast-2.11.0+-x64-linux.tar.gz\uff09 tar -xzvf rmblast-2.11.0+-x64-linux.tar.gz <\/code><\/pre>\n<h5>3\u3001RepeatMasker\u7684\u5b89\u88c5<\/h5>\n<pre class=\"language-java prettyprint linenums\"><code>#\u4e0b\u8f7d tar xzvf RepeatMasker-4.1.2-p1.tar.gz cd RepeatMasker chmod -R 755 * #\u7f16\u8bd1 .\/configure # \u6dfb\u52a0\u5230\u73af\u5883\u53d8\u91cf\u4e2d vi ~\/.bashrc export PATH=\"$PATH:\/home\/nieyimeng\/biosoft\/RepeatMasker\" source ~\/.bashrc <\/code><\/pre>\n<h3>\u4e8c\u3001RepeatMoleder\u7684\u5b89\u88c5<\/h3>\n<h5>1\u3001\u5b89\u88c5RepeatMasker\u3001TRF\u3001RMblast<\/h5>\n<h5>2\u3001\u5b89\u88c5RECON<\/h5>\n<pre class=\"language-java prettyprint linenums\"><code>wget -c http:\/\/www.repeatmasker.org\/RepeatModeler\/RECON-1.08.tar.gz tar -xzvf RECON-1.08.tar.gz cd RECON-1.08\/src make <\/code><\/pre>\n<h5>3\u3001\u5b89\u88c5RepeatScount<\/h5>\n<pre class=\"language-java prettyprint linenums\"><code>wget -c http:\/\/www.repeatmasker.org\/RepeatScout-1.0.6.tar.gz tar -zxvf RepeatScout-1.0.6.tar.gz cd RepeatScout-1.0.6 make <\/code><\/pre>\n<h5>4\u3001\u53ef\u9009\u8f6f\u4ef6\uff0c\u8fd0\u884cLTR\u7ed3\u6784\u641c\u7d22\u5fc5\u987b\u8f6f\u4ef6\uff0c\u4e5f\u53ef\u4ee5\u4e0d\u5b89\u88c5<\/h5>\n<h5>4.1\u3001LtrHarvest\uff0cLtrHarvest\u7a0b\u5e8f\u662fGenomeTools\u5957\u4ef6\u7684\u4e00\u90e8\u5206\uff0c\u5b89\u88c5genometools\u5373\u53ef<\/h5>\n<pre class=\"language-java prettyprint linenums\"><code>wget -c http:\/\/genometools.org\/pub\/genometools-1.5.9.tar.gz tar -zxvf genometools-1.5.9.tar.gz cd genometools-1.5.9 make threads=yes <\/code><\/pre>\n<h5>4.2\u3001Ltr_retriever<\/h5>\n<pre class=\"language-java prettyprint linenums\"><code>#\u4e0b\u8f7d\u5730\u5740\uff08https:\/\/github.com\/oushujun\/LTR_retriever\/archive\/master.zip)` unzip LTR_retriever-master.zip <\/code><\/pre>\n<h5>4.3\u3001MAFFT<\/h5>\n<pre class=\"language-java prettyprint linenums\"><code>#\u4e0b\u8f7d\u5730\u5740\uff08https:\/\/mafft.cbrc.jp\/alignment\/software\/mafft-7.487-with-extensions-src.tgz) tar xfvz mafft-7.487-with-extensions-src.tgz cd mafft-7.487-with-extensions\/core\/ vi Makefile (any other text editor is ok.) #\u7b2c\u4e00\u884c From: PREFIX = \/usr\/local To: PREFIX = \/home\/your_home\/somewhere (must be absolute path) #\u7b2c\u4e09\u884c From: BINDIR = $(PREFIX)\/bin To: BINDIR = \/home\/your_home\/bin (or elsewhere in your command-search path) #\u6709sudo\u6743\u9650\u53ef\u4ee5\u76f4\u63a5sudo\u5b89\u88c5 sudo apt install mafft <\/code><\/pre>\n<h5>4.4\u3001CD-HIT<\/h5>\n<pre class=\"language-java prettyprint linenums\"><code>#\u4e0b\u8f7d\u5730\u5740\uff08https:\/\/github.com\/weizhongli\/cdhit\/archive\/master.zip\uff09 unzip cdhit-master.zip cd cdhit-master make <\/code><\/pre>\n<h5>4.5\u3001Ninja<\/h5>\n<pre class=\"language-java prettyprint linenums\"><code>#\u4e0b\u8f7d\u5730\u5740\uff08https:\/\/github.com\/TravisWheelerLab\/NINJA\/releases\/tag\/0.95-cluster_only\uff09 unzip NINJA-0.95-cluster_only.zip cd NINJA-0.95-cluster_only cd NINJA make all <\/code><\/pre>\n<h5>4.6\u3001twoBitToFa, faToTwoBit, twoBitInfo<\/h5>\n<pre class=\"language-java prettyprint linenums\"><code>#twoBitToFa(http:\/\/hgdownload.cse.ucsc.edu\/admin\/exe\/linux.x86_64\/twoBitToFa) #faToTwoBit(http:\/\/hgdownload.cse.ucsc.edu\/admin\/exe\/linux.x86_64\/faToTwoBit) #twoBitInfo(http:\/\/hgdownload.cse.ucsc.edu\/admin\/exe\/linux.x86_64\/twoBitInfo) mkdir UCSCTOOLS chmod 755 * #\u5c06\u4e09\u4e2a\u6587\u4ef6\u653e\u5728\u65b0\u5efa\u7684UCSCTOOLS\u6587\u4ef6\u5939\u4e2d <\/code><\/pre>\n<h5>5\u3001RepeatModeler\u5b89\u88c5<\/h5>\n<pre class=\"language-java prettyprint linenums\"><code>#\u4e0b\u8f7d\u5730\u5740\uff08http:\/\/www.repeatmasker.org\/RepeatModeler\/RepeatModeler-2.0.2a.tar.gz\uff09 tar -zxvf RepeatModeler-2.0.2a.tar.gz cd RepeatModeler-2.0.2a perl .\/configure #\u8bbe\u7f6e\u5404\u5b89\u88c5\u6587\u4ef6\u4f4d\u7f6e\u3002\u6ce8\u610f\u4e00\u4e9b\u5730\u5740\u662fsrc\u4e0b\uff0c\u4e00\u4e9b\u5730\u5740\u662fbin\uff0c\u4e00\u4e9b\u662f\u6587\u4ef6\u76ee\u5f55\u4e0b RECON_DIR:\/public\/home\/huangyuan_nym\/biosoft\/RECON-1.08\/src RSCOUT_DIR:\/public\/home\/huangyuan_nym\/biosoft\/RepeatScout-1.0.6 TRF_PRGM: \/public\/home\/huangyuan_nym\/biosoft\/TRF-master\/build\/src\/trf CD-HIT_DIR:\/public\/home\/huangyuan_nym\/biosoft\/cdhit-master UCSCTOOLS_DIR: \/public\/home\/huangyuan_nym\/biosoft\/UCSCTOOLS\/ RMBLAST_DIR: \/public\/home\/huangyuan_nym\/biosoft\/rmblast-2.11.0\/bin GENOMETOOLS_DIR: \/public\/home\/huangyuan_nym\/biosoft\/genometools-1.5.9\/bin LTR_RETRIEVER_DIR: \/public\/home\/huangyuan_nym\/biosoft\/LTR_retriever-master MAFFT_DIR:\/public\/home\/huangyuan_nym\/biosoft\/mafft-7.487-with-extensions\/core NINJA_DIR: \/public\/home\/huangyuan_nym\/biosoft\/NINJA-0.95-cluster_only\/NINJA <\/code><\/pre>\n<h3>\u4e09\u3001\u5b89\u88c5\u9047\u5230\u95ee\u9898\u8865\u5145<\/h3>\n<h5>\u95ee\u9898\uff1a\u62a5\u9519\uff0c\u9700\u8981\u5b89\u88c5\u4e00\u4e2aperl\u6a21\u5757 Devel::Size<\/h5>\n<p>#Can\u2019t locate Devel\/Size.pm in @INC (@INC contains: \/public\/home\/huangyuan_nym\/biosoft\/RepeatMasker \/public\/home\/huangyuan_nym\/biosoft\/RepeatModeler-2.0.2a \/usr\/lib\/perl5\/site_perl \/usr\/local\/lib64\/perl5 \/usr\/local\/share\/perl5 \/usr\/lib64\/perl5\/vendor_perl \/usr\/share\/perl5\/vendor_perl \/usr\/lib64\/perl5 \/usr\/share\/perl5 .) at .\/RepeatModeler line 140<\/p>\n<h5>\u89e3\u51b3\uff1a\u5728\u4e2a\u4eba\u8d26\u6237\u4e0b\u5b89\u88c5perl\u6a21\u5757<\/h5>\n<pre class=\"language-java prettyprint linenums\"><code>#\u4e0b\u8f7d\u8be5\u6a21\u5757\uff08https:\/\/cpan.metacpan.org\/authors\/id\/N\/NW\/NWCLARK\/Devel-Size-0.83.tar.gz\uff09 tar -zxvf Devel-Size-0.83.tar.gz perl Makefile.PL INSTALL_BASE=\/public\/home\/huangyuan_nym\/perl5 make make install #\u53ef\u4ee5\u5728CPAN.pm\u914d\u7f6e\u4e2d\u8fdb\u884c\u8bbe\u7f6e\uff0c\u4ee5\u4fbf\u5728\u4f7f\u7528CPAN.pm shell\u65f6\u6a21\u5757\u81ea\u52a8\u5b89\u88c5\u5728\u79c1\u6709\u5e93\u76ee\u5f55\u4e2d % cpan cpan&gt; o conf makepl_arg INSTALL_BASE=\/public\/home\/huangyuan_nym\/perl5 cpan&gt; o conf commit #\u5728\u73af\u5883\u53d8\u91cf\u4e2d\u6dfb\u52a0\u5e93\u7684\u4f4d\u7f6e vi ~\/.bashrc #\u5728\u6700\u540e\u4e00\u884c\u6dfb\u52a0 export PERL5LIB=\/public\/home\/huangyuan_nym\/perl5\/lib\/perl5 <\/code><\/pre>\n<h5>\u6ce8\uff1a\u5982\u679c\u4e00\u76f4\u62a5\u9519\uff0c\u53ef\u4ee5\u5c1d\u8bd5\u4f7f\u7528RepeatModeler\u4e4b\u524d\u7684\u7248\u672c\u8fdb\u884c\u7f16\u8bd1\u5b89\u88c5\u3002<\/h5>\n","protected":false},"excerpt":{"rendered":"reaper\u8f6f\u4ef6\u5b89\u88c5_CurseForge\u6574\u5408\u5305\u5b89\u88c5RepeatModeler\u7684\u5b89\u88c5\uff08\u5305\u542bRepeatMasker\u5b89\u88c5\uff09nym2021-8-15RepeatMasker\u5b98\u7f51\u5730\u5740\uff08http:...","protected":false},"author":1,"featured_media":0,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"footnotes":""},"categories":[],"tags":[],"_links":{"self":[{"href":"https:\/\/mushiming.com\/wp-json\/wp\/v2\/posts\/5317"}],"collection":[{"href":"https:\/\/mushiming.com\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/mushiming.com\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/mushiming.com\/wp-json\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"https:\/\/mushiming.com\/wp-json\/wp\/v2\/comments?post=5317"}],"version-history":[{"count":0,"href":"https:\/\/mushiming.com\/wp-json\/wp\/v2\/posts\/5317\/revisions"}],"wp:attachment":[{"href":"https:\/\/mushiming.com\/wp-json\/wp\/v2\/media?parent=5317"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/mushiming.com\/wp-json\/wp\/v2\/categories?post=5317"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/mushiming.com\/wp-json\/wp\/v2\/tags?post=5317"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}