search

dpuiu / MitoHPC

MIT License
10 stars 12 forks source link

Change to install_prerequisites.sh prevents it from installing #1

Open timshall opened 2 years ago

timshall commented 2 years ago

Hi,

Thank you for putting this pipeline together, we're hoping to perform some great research with it. I noticed today some trouble with installing the prerequisite tools for mitoHPC and narrowed down the issue to scripts/install_prerequisites.sh wherein a recent commit changed

set -x

to

set -e

Before any installing a tool, the command which is run which gives an exit status of 1 if the tool has no path and is not installed. This leads to the script exiting due to set -e and not installing any tools that aren't already installed.

I assume this is an unintended change so thought best to note this.

Tim

dpuiu commented 1 year ago

Thank you Tim, you are right. I will incorporate the change. Sorry for the late reply.

Daniela Puiu

Bioinformatics Engineer

Department of Biomedical Engineering

Johns Hopkins University

From: timshall @.> Sent: Wednesday, July 13, 2022 10:59 AM To: dpuiu/MitoHPC @.> Cc: Subscribed @.***> Subject: [dpuiu/MitoHPC] Change to install_prerequisites.sh prevents it from installing (Issue #1)

  External Email - Use Caution

Hi,

Thank you for putting this pipeline together, we're hoping to perform some great research with it. I noticed today some trouble with installing the prerequisite tools for mitoHPC and narrowed down the issue to scripts/install_prerequisites.sh wherein a recent commit changed

set -x

to

set -e

Before any installing a tool, the command which is run which gives an exit status of 1 if the tool has no path and is not installed. This leads to the script exiting due to set -e and not installing any tools that aren't already installed.

I assume this is an unintended change so thought best to note this.

Tim

— Reply to this email directly, view it on GitHubhttps://nam02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fdpuiu%2FMitoHPC%2Fissues%2F1&data=05%7C01%7Cdpuiu%40jhu.edu%7C935a758440d74d87b6d008da64e05fb6%7C9fa4f438b1e6473b803f86f8aedf0dec%7C0%7C0%7C637933212087200557%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=PT3XWDy%2B7BDCxYJUegShkmWW4Ds65R9uo0o3j4X7HsA%3D&reserved=0, or unsubscribehttps://nam02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fnotifications%2Funsubscribe-auth%2FAAHXHMZVOA5MX5DXBP5UIZTVT3KWLANCNFSM53PBMAZA&data=05%7C01%7Cdpuiu%40jhu.edu%7C935a758440d74d87b6d008da64e05fb6%7C9fa4f438b1e6473b803f86f8aedf0dec%7C0%7C0%7C637933212087200557%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=FcLXQPMlO5jkKFwDSoUDHpSAk38hiFUKlrbzqoxwHE0%3D&reserved=0. You are receiving this because you are subscribed to this thread.Message ID: @.***>