Picard Tools runs out of space when running Poolparty pipeline

Question

[Dracaena]

Hi all,

I am using a pipeline to align and analyze NGS data called "Poolparty" ( https://github.com/StevenMicheletti/poolparty ). Overall it's a great way to do so since it delivers both VCF and sync (popoolation) files. The only problem is, that I don't have enough space in my /tmp directory and this causes issues when Picard Tools starts running. I am running linux on windows as an app (Ubuntu for windows) and the disc on which my home folder is on is tight in space. So here's my question: Is there I way to set my /tmp directory to another (external) hard drive? Or can I add an argument to the script somehow so Picard Tools knows which folder to use as TEMP folder. I know if you use Picard Tools alone you can set "TEMP_DIR path"

Many thanks

[Pierre Lindenbaum]

I know if you use Picard Tools alone you can set "TEMP_DIR path"

so, why don't you use this parameter ?

[h.mon]

One can set a temporary folder for Picard (see Out Of Disk Space With Picard Tools ? and picard-tools MarkDuplicates - spilling to disk). You may have to hack PoolParty, but it should be pretty easy to add a command-line option to it.

You can also try the suggestion from How to change default /tmp to /home/user/tmp.

Answer 1

[Dracaena]

Ok guys, I just tried adding the TMP_DIR in the config file and it worked. Picard Tools used that DIR as temp. Poolparty does not mention that this is possible, but apparantly it is. Nice!