更加方便的安装方法用Bioconda安装好cd-hit repeatmasker, 然后下载LTR_retriever: conda create -n LTR_retriever source activate LTR_retriever conda install -c conda-forge perl perl-text-soundex conda install -c bioconda cd-hit conda install -c bioconda/label/cf201901 repeatmasker git clone https://g...
$conda create -n LTR_retriever $conda activate LTR_retriever $conda install -y -c conda-forge perl perl-text-soundex $conda install -y -c bioconda cd-hit repeatmasker $git clone https://github.com/oushujun/LTR_retriever.git $./LTR_retriever/LTR_retriever -h 除此之外还需要安几个依赖的软...
conda env create -f /your_path_to/LTR_retriever/LTR_retriever.yml Alternatively, you may use the conda recipe, but due to the large number of dependencies, conda solve may take hours... Unfortunately, the conda recipe currently could not be installed properly withmamba. ...
Step by step using conda Standard installation Inputs Outputs Usage Citations Introduction LTR_retriever is a command line program (in Perl) for accurate identification of LTR retrotransposons (LTR-RTs) from outputs of LTRharvest, LTR_FINDER, MGEScan 3.0.0, LTR_STRUC, and LtrDetector, and gene...
Update ltr_retriever - unpin repeatmasker pin <4.1.5 General instructions If this PR adds or updates a recipe, use "Add" or "Update" appropriately as the first word in its title. New recipes not directly relevant to the biological sciences need to be submitted to theconda-forge channel...
同样用conda安装了LTR_FINDER;按照教程完成了第一步的分析。 但是第二步时(LTR_retriever -threads 4 -genome Athaliana.fa -infinder Athaliana.finder.scn),报错,原因为:Dependency checking: Error: The RMblast engine is not installed in RepeatMasker!
conda install-c bioconda/label/cf201901 repeatmasker git clone https://github.com/oushujun/LTR_retriever.git./LTR_retriever/LTR_retriever-h 此外你还需要额外安装LTRharvest,LTR_FINDER和MGEScan_LTR。 LTRharverst:http://genometools.org/ LTR_FINDER:https://github.com/xzhub/LTR_Finder ...
blast+: quickly install byconda install blast TEsorter: git clone https://github.com/zhangrengang/TEsorter cd TEsorter python setup.py install Quick Start # run the example TEsorter-test # or TEsorter TEsorter/test/rice6.9.5.liban
conda create -n LTR_retriever conda activate LTR_retriever conda install -y -c conda-forge perl perl-text-soundex conda install -y -c bioconda cd-hit repeatmasker git clone https://github.com/oushujun/LTR_retriever.git ./LTR_retriever/LTR_retriever -h chmod 757 gt-1.6.2/bin/gt chmod 75...
Install LTR_retriever gitclonehttps://github.com/oushujun/LTR_retriever.git 或者使用conda安装LTR_retriever conda create-nLTR_retrieverconda activateLTR_retrieverconda install-c conda-forge perl perl-text-soundex conda install-c bioconda cd-hit repeatmasker ...