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. ...
Conda is able to record and lock (a.k.a. pin) dependency versions used at build time of other recipes. This way, one can avoid that expectations of a downstream recipe with regards to API, ABI, or CLI are violated by later changes in the recipe. If not already present in the meta....
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 -c bioconda cd-hit repeatmasker git clone...
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 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 ...
Quick installation using conda 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_STRU...
$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....
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 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...