Commit b1fa83a9 authored by Pradat Yoann's avatar Pradat Yoann

update README with install details

parent e591e5df
......@@ -51,11 +51,11 @@ perl INSTALL.pl
The perl script INSTALL.pl may return errors as missing dependencies or other. For instance,the error `Bio::Root::Version is not installed` may be solved by running `sudo cpanm Bio::Root::Version`. You may have more than one such library to install. Refer to the github for the details.
The installation from the perl script offers the choice to install cache files (most efficient use of vep) and FASTA files (to retrieve sequence data for HGVS notations) into `$HOME/.vep`. You may also install plugins for additional analyses. Download cache files for Homo Sapiens genome 99_GRCh37 (or newer). The total download size is about 12 GB of data so a stable and fast connection is required here. The FASTA file Homo_sapiens.GRCh37.75.dna.primary_assembly.fa.gz requires 882 MB of storage. *DO NOT FORGET* to unzip this file (or VEP will fail).
The installation from the perl script offers the choice to install cache files (most efficient use of vep) and FASTA files (to retrieve sequence data for HGVS notations) into `$HOME/.vep`. You may also install plugins for additional analyses. Download cache files for Homo Sapiens genome 100_GRCh37 (or newer). The total download size is about 12 GB of data so a stable and fast connection is required here. The uncompressed FASTA file (**DO NOT FORGET** to uncompress this file or VEP will fail) Homo_sapiens.GRCh37.75.dna.primary_assembly.fa.gz requires about 3.0 GB of storage.
### 2.2 Install vcf2maf
VEP is required by vcf2maf may you need also need the set of commands `samtools`, and `htslib` available at [http://www.htslib.org/download/](http://www.htslib.org/download/). Do the following
VEP is required by vcf2maf but you also need the commands from `samtools` and `htslib` available at [http://www.htslib.org/download/](http://www.htslib.org/download/). Do the following
```
cd samtools-1.x
......
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