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...
RepeatMasker (会自动安装所以来的TRF和RMblast) 所以偷懒,依次用conda安装了上述软件。 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 ...
conda install -c bioconda ltr_retriever Step by step using conda You may use conda to quickly install all dependencies and LTR_retriever is then good to go: conda create -n LTR_retriever conda activate LTR_retriever conda install -y -c conda-forge perl perl-text-soundex conda install -y -...
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 with mamba. conda install -c...
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...
$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件 1.makeblastdb,blastn,andblastxintheBLAST+package(ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/)2....
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
LTR Retriever crashes when input assembly does not contain LTRs Plant-Food-Research-Open/assemblyqc#92 Closed SPPearce reviewed Jul 16, 2024 View reviewed changes modules/nf-core/ltrharvest/tests/tags.yml Outdated Contributor SPPearce Jul 16, 2024 Why have you deleted the tags file? Memb...
上述软件自行下载,或者使用conda进行安装即可 安装LTR_retriever git clone https://github.com/oushujun/LTR_retriever.git 进入paths文件,修改各个软件所在路径 BLAST+=/data/pub/liuzy/software/ncbi-blast-2.8.1+/bin/ #a path that contains makeblastdb, blastn, blastx ...