Question: Unable to configure SRA toolkit in cygwin
0
gravatar for mad.irish.frog
2.8 years ago by
mad.irish.frog0 wrote:

Hello, first post!

I'm trying to download SRA data using cygwin and SRA tools. If I get the data down, I can do everything I want to do, but downloading the data is where I'm getting caught up. I'm trying to change the location that prefetch downloads files to a network location instead of my hard drive which fills up fast. Cygwin's default location is c:/ncbi

  1. did a "full" cygwin installation (-debug, -docs) ~15GB
  2. curl -OL http://ftp-trace.ncbi.nlm.nih.gov/sra/sdk/2.7.0/sratoolkit.2.7.0-win64.zip
  3. unzip sratoolkit.2.7.0-win64.zip
  4. cd sratoolkit.2.7.0-win64/bin
  5. ls produces many things including vdb-config.exe
  6. ./vdb-config -i on my local machine produces "-bash: ./vdb-config: Permission denied" I have total read-write permissions on my own machine
  7. If I try to unzip within the network site (questionable if I have the power to do this), I can certainly unzip the files and produce the same list of executables, but when I try to change the configuration I get "$ ./vdb-config -i ok Segmentation fault"

I'm sure I'm doing something incredibly stupid, but any suggestions would be appreciated.

software error • 1.2k views
ADD COMMENTlink modified 2.8 years ago by Antonio R. Franco4.0k • written 2.8 years ago by mad.irish.frog0

You probably need to chmod a+x vdb-config, or whatever the equivalent is in cygwin.

ADD REPLYlink written 2.8 years ago by Devon Ryan90k

ok, now I'm getting $ ./vdb-config -i ok Segmentation fault

for the one on my local machine. I've removed the folder in terminal ($ rm -rf sratoolkit.2.7.0-win64/) and unzipped again and now I'm getting the same errror. I also tried redownloading the .zip file again and re-unzipping (thinking I had a bad zip file) and I keep getting errors. Thanks though!

ADD REPLYlink written 2.8 years ago by mad.irish.frog0
1

No clue, you'll have better luck borrowing someone's Mac or Linux computer. Little in bioinformatics supports windows.

ADD REPLYlink written 2.8 years ago by Devon Ryan90k

I use sra tools from cygwin. Have you set SRA_PATH=`cygpath -u C:/<whatever>/sratoolkit.X.Y.Z-win64/bin in .bashrc or are you running it as a cygwin tool?

It is a ballache though, even once it runs it's really slow (the ballache is OS-independent). I'm sure I'll have my set up notes somewhere

ADD REPLYlink modified 2.8 years ago • written 2.8 years ago by russhh4.5k
1
gravatar for Antonio R. Franco
2.8 years ago by
Spain. Universidad de Córdoba
Antonio R. Franco4.0k wrote:

This is a case where the new native Ubuntu Linux implemented into Windows 10 anniversary update comes handy

ADD COMMENTlink written 2.8 years ago by Antonio R. Franco4.0k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1484 users visited in the last hour