Question: Unable to configure SRA toolkit in cygwin
0
gravatar for mad.irish.frog
12 months 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 • 443 views
ADD COMMENTlink modified 12 months ago by Antonio R. Franco3.4k • written 12 months ago by mad.irish.frog0

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

ADD REPLYlink written 12 months ago by Devon Ryan70k

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 12 months 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 12 months ago by Devon Ryan70k

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 12 months ago • written 12 months ago by russhh2.6k
1
gravatar for Antonio R. Franco
12 months ago by
Spain. Universidad de Córdoba
Antonio R. Franco3.4k wrote:

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

ADD COMMENTlink written 12 months ago by Antonio R. Franco3.4k
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