Fwd: no abyss-pe.Makefile in (/.conda/envs/abyss/bin)

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Sabrin Abdelghany

Sep 6, 2022, 1:38:47 PM9/6/22
to abyss-users

From: "Sabrin Abdelghany" <sabrin.a...@leibniz-zmt.de>
To: "abyss-users" <abyss...@googlegroups.com>
Sent: Tuesday, September 6, 2022 1:56:44 PM
Subject: no abyss-pe.Makefile in (/.conda/envs/abyss/bin)

Hi there,

Any suggestion please why i receive this error message running abyss with multiple libraries 

which: no abyss-pe.Makefile in (/user/asga9989/.conda/envs/abyss/bin)
dirname: missing operand
Try 'dirname --help' for more information.

(abyss) [asga9989@hpcl001 trim]$ cd /user/asga9989/.conda/envs/abyss/bin
(abyss) [asga9989@hpcl001 bin]$ abyss-pe.Makefile --help
-bash: /user/asga9989/.conda/envs/abyss/bin/abyss-pe.Makefile: Permission denied
Any suggestions please what to do to skip this error?

Best Regarding 

image (1).png

Lauren Coombe

Sep 6, 2022, 1:55:19 PM9/6/22
to ABySS
Hi Sabrin,

To launch ABySS, use `abyss-pe`, not `abyss-pe.Makefile`. The latter is generated to ensure ABySS works in a conda installation, but we always use `abyss-pe` when running ABySS.

Hope that helps - thank you for your interest in ABySS!

Asad Karim

Sep 7, 2022, 11:55:39 AM9/7/22
to Lauren Coombe, ABySS
Use docker image of abyss


With best regards,
Asad Karim, PhD.

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Lauren Coombe

Sep 7, 2022, 11:59:39 AM9/7/22
to ABySS
Hi Asad,

Thank you for mentioning that! Yes, there are multiple options for running ABySS, including conda, docker, homebrew and compiling from the source code. Note that we recommend using the biocontainers docker image if you go the docker route (https://quay.io/repository/biocontainers/abyss).
Sabrin also opened a github issue, so we'll continue any conversation there: https://github.com/bcgsc/abyss/issues/455 


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