useuse

[aidenlab]

useuse

[coreywischmeyer]

I see there was just a new release, I'll check that out too.

[nchernia]

The paths and load commands up top need to be adjusted for your system. On our version of UGE, we need to call "use" to load modules. Ask your cluster administrator what you need to do to load BWA, Java, and CUDA/GPUs (if applicable), then modify the script as appropriate.

…

On Fri, Aug 11, 2017 at 11:53 PM Corey Wischmeyer ***@***.***> wrote: I see there was just a new release, I'll check that out too. — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#25 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/ABWiW-qC8knfTg5-SGPvL53OaaVRBfq0ks5sXM1BgaJpZM4O1JNW> .

[coreywischmeyer]

Sadly, I am the cluster manager, in that I installed SGE and configured it for the sole purpose of using Juicer. I've used it before on previous projects and I don't remember a module system. SGE also appears to be able to find my version of BWA without issue. I was hesitant to try out the CPU version as it's in beta, but I'll see if I can get that going.

[nchernia]

So just get rid of that line. If you can find BWA and Java no problem, then delete anything up top that fails in that regard.

…

On Mon, Aug 14, 2017 at 5:23 PM, Corey Wischmeyer ***@***.***> wrote: Sadly, I am the cluster manager, in that I installed SGE and configured it for the sole purpose of using Juicer. I've used it before on previous projects and I don't remember a module system. SGE also appears to be able to find my version of BWA without issue. I was hesitant to try out the CPU version as it's in beta, but I'll see if I can get that going. — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#25 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/ABWiWyeuRgwVZ0eZvmgS667_DfStVAwrks5sYGZfgaJpZM4O1JNW> .

-- Neva Cherniavsky Durand, Ph.D. Staff Scientist, Aiden Lab www.aidenlab.org

[coreywischmeyer]

Yes, you are correct, removing all instances of $usePath and changing this bit

usePath=/broad/software/scripts/useuse
load_bwa="use .bwa-0.7.12"
load_java="use Java-1.8"
load_cluster="use UGER"
load_coreutils="use Coreutils"

to this

load_bwa=""
load_java=""
load_cluster=""
load_coreutils=""

Moved me further into the script, but then I started running into issues with split (our version is out of date).

So I have switched to using the CPU version for now, and submitted some of the changes I need to make as my first pull request.