/tmp issues

[Dr. M.D. Sharma]

Hi Folks,

We have a failry small /tmp directory so I usually export the TMP/TMPDIR/TEMP variables to an appropriate tmp folder instead of the default /tmp. It works in most cases but Trans-Abyss seems bent on using /tmp no matter hw many times I declare TMPpaths.. has anyone seen this issue / have a solution?

Cheers,

MD

[Ka Ming Nip]

Hi,

The only components that uses the tmp directory is the ABySS modules and probably unix sort.

So, setting the environment variable `TMPDIR` as described in the link below would be sufficient, but I would use your working directory instead of `/var/tmp`.

https://github.com/bcgsc/abyss/blob/master/README.md#before-starting-an-assembly

Ka Ming

--
Ka Ming Nip
Graduate Student | Dr. Inanc Birol Lab
Canada's Michael Smith Genome Sciences Centre

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From: trans...@googlegroups.com <trans...@googlegroups.com> on behalf of Dr. M.D. Sharma <manmo...@gmail.com>
Sent: September 24, 2018 5:46 AM
To: Trans-ABySS
Subject: /tmp issues

 

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