Error message with end-to-end

[RaviKDinesh]

I'm interested in using CLD to make a custom library, however, whenever I try to run end_to_end, I keep receiving an error message below:

$ docker run -v ~/Desktop:/data boutroslab/cld_docker cld --task=end_to_end --output-dir=. --parameter-file=./params.txt --gene-list=gene_list.txt
Possible precedence issue with control flow operator at /usr/local/share/perl/5.26.1/Bio/DB/IndexedBase.pm line 845.
The gene list file gene_list.txt could not be opened. Either the user has no rights the read it or the file does not exist. at /usr/bin/cld line 1741.

This happens whether I'm running this on my desktop or using my university's cluster. I have used both my own custom gene list as well as the sample one provided and I still receive this error message. Any advice?

[fheigwer]

Hi there, If your gene_list file is on your desktop then it should be —gene-list=./gene_list.txt or better /data/gene_list.txt Let me know if it still does not work. Best, Florian Am 12.04.2020 um 04:34 schrieb RaviKDinesh <notifications@github.com>:  I'm interested in using CLD to make a custom library, however, whenever I try to run end_to_end, I keep receiving an error message below: $ docker run -v ~/Desktop:/data boutroslab/cld_docker cld --task=end_to_end --output-dir=. --parameter-file=./params.txt --gene-list=gene_list.txt Possible precedence issue with control flow operator at /usr/local/share/perl/5.26.1/Bio/DB/IndexedBase.pm line 845. The gene list file gene_list.txt could not be opened. Either the user has no rights the read it or the file does not exist. at /usr/bin/cld line 1741. This happens whether I'm running this on my desktop or using my university's cluster. I have used both my own custom gene list as well as the sample one provided and I still receive this error message. Any advice? — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub<#17>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/ABAJUGNNXM33IRPZKEJHCL3RMESC3ANCNFSM4MGHSMYQ>.

[RaviKDinesh]

Hi Florian,

Thank you for the quick reply. I have all the files: params.txt, gene_list.txt, and the database (mus_musculus.tar.gz, downloaded from the provided link) all in one folder. When I send the command I am in the folder, so I think it shouldn't be the problem. I have tried specifying the path to the files in a number of ways (including the ones you just mentioned in your response) and I keep getting the same error message. This also happens when I try it on the university cluster (using singularity) and running on an the image.

I am new to docker, so I'm not sure where "~/Desktop:/data" is, since the file doesn't exist. I created a file named data, moved my files to it, and tried to run the command again and got the same error message.

My apologies if there is something really basic I am not understanding. Any advice you can offer is appreciated.

Mya po

[fheigwer]

Dear Mya po, The matter is to get the principle of docker containers right. They are a computer inside a computer. However they only “see” their files and not yours (the computer they are inside). You can make them “see” a folder by mounting it with this command option “–v /path/to/my/folder:/folder/on/docker” this means in your case that the folder “~/Desktop:/data” means that the folder /Users/user/Desktop (standard desktop on a mac) is now named /data in the container. When you give it an input file it needs the docker path to it. So give it –gene-list=/data/gene_list.txt means that gene_list.txt should be in /Users/user/Desktop on the host computer (the one you work with). If you email me from your email address I can send you a more detailed chapter on how to do this via email. Best, Florian

…

------------------------------------------ Dr. Florian Heigwer German Cancer Research Center (DKFZ) Signaling and Functional Genomics/B110 Post-Doc Management Board: Prof. Dr. med. Michael Baumann, Ursula Weyrich VAT-ID No.: DE143293537 From: RaviKDinesh <notifications@github.com> Reply-To: boutroslab/cld <reply@reply.github.com> Date: Monday, 13. April 2020 at 01:30 To: boutroslab/cld <cld@noreply.github.com> Cc: Florian Heigwer <florian_heigwer@web.de>, Comment <comment@noreply.github.com> Subject: Re: [boutroslab/cld] Error message with end-to-end (#17) Hi Florian, Thank you for the quick reply. I have all the files: params.txt, gene_list.txt, and the database (mus_musculus.tar.gz, downloaded from the provided link) all in one folder. When I send the command I am in the folder, so I think it shouldn't be the problem. I have tried specifying the path to the files in a number of ways (including the ones you just mentioned in your response) and I keep getting the same error message. This also happens when I try it on the university cluster (using singularity) and running on an the image. I am new to docker, so I'm not sure where "~/Desktop:/data" is, since the file doesn't exist. I created a file named data, moved my files to it, and tried to run the command again and got the same error message. My apologies if there is something really basic I am not understanding. Any advice you can offer is appreciated. Mya po — You are receiving this because you commented. Reply to this email directly, view it on GitHub<#17 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/ABAJUGMVIC7BKCFM6MQ63VTRMJFJ5ANCNFSM4MGHSMYQ>.