search

DRL / blobtools

Modular command-line solution for visualisation, quality control and taxonomic partitioning of genome datasets
GNU General Public License v3.0
187 stars 44 forks source link

Could not download NCBI taxdump. #70

Closed drashutosh closed 6 years ago

drashutosh commented 6 years ago

Hi I am trying to install blobtools and I am finding following issue 

Python dependencies installed.
[+] Creating BlobTools executable...done.
[+] Downloading samtools-1.5...done.
[+] Unpacking samtools-1.5...done.
[+] Configuring samtools-1.5...done.
[+] Compiling samtools-1.5...done.
[+] Cleaning up...
[+] Downloading NCBI taxdump from ftp://ftp.ncbi.nlm.nih.gov/pub/taxonomy/taxdump.tar.gz ...FAIL.

Any suggestions Thanks in advance

DRL commented 6 years ago

Hi drashutosh,

the install script has been unable to download the NCBI taxdump.

you can simply download it by hand :

# set DIR to path of blobtools on your system
DIR=/path/to/blobtools
# download taxdump 
wget ftp://ftp.ncbi.nlm.nih.gov/pub/taxonomy/taxdump.tar.gz
# mv to blobtools folder
mv taxdump.tar.gz $DIR/data/
# unpack nodes/names
tar zxf $DIR/data/taxdump.tar.gz -C $DIR/data/ nodes.dmp names.dmp
# create nodesdb
$DIR/blobtools nodesdb --nodes $DIR/data/nodes.dmp --names $DIR/data/names.dmp

let me know if this works for you.

cheers,

dom