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

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Sabrin Abdelghany

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Sep 6, 2022, 1:38:47 PM9/6/22
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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 
Sabrin

image (1).png

Lauren Coombe

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Sep 6, 2022, 1:55:19 PM9/6/22
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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!
Lauren

Asad Karim

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


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With best regards,
________________________
Asad Karim, PhD.
   

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Lauren Coombe

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Sep 7, 2022, 11:59:39 AM9/7/22
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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 

Cheers,
Lauren

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