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CompSynBioLab-KoreaUniv / FunGAP

FunGAP: fungal Genome Annotation Pipeline
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Error building docker image #99

Closed Debatosh closed 10 months ago

Debatosh commented 10 months ago

Hello, I was trying to build the docker image using bash. However, I am running into the following error: (base) d@deb:/mnt/d/pacbio/FunGAP/docker$ docker build -t fungap . [+] Building 1.5s (10/11) docker:default => [internal] load build definition from Dockerfile 0.0s => => transferring dockerfile: 546B 0.0s => [internal] load .dockerignore 0.0s => => transferring context: 2B 0.0s => [internal] load metadata for docker.io/taniguti/fungap-base:v1.1.1 0.8s => [auth] taniguti/fungap-base:pull token for registry-1.docker.io 0.0s => [1/6] FROM docker.io/taniguti/fungap-base:v1.1.1@sha256:b84460e6c8b3b2feda78014a8e4e6a9e224599163fdc70e4c09ba58303312cd7 0.0s => [internal] load build context 0.2s => => transferring context: 18.28MB 0.2s => CACHED [2/6] COPY gmes_linux_64.tar.gz /workspace/FunGAP/external/ 0.0s => CACHED [3/6] COPY gm_key_64.gz /workspace/FunGAP/external/ 0.0s => CACHED [4/6] WORKDIR /workspace/FunGAP/external/ 0.0s => ERROR [5/6] RUN tar -zxvf gmes_linux_64_4.tar.gz && gunzip gm_key_64.gz && cp gm_key_64 ~/.gm_key && cd /workspace/FunGAP/external/gmes_linux_64 0.4s

[5/6] RUN tar -zxvf gmes_linux_64_4.tar.gz && gunzip gm_key_64.gz && cp gm_key_64 ~/.gm_key && cd /workspace/FunGAP/external/gmes_linux_64_4/ && cp other/reformat_fasta.pl . && perl change_path_in_perl_scripts.pl "/usr/bin/env perl": 0.297 tar (child): gmes_linux_64_4.tar.gz: Cannot open: No such file or directory 0.297 tar (child): Error is not recoverable: exiting now 0.297 tar: Child returned status 2 0.297 tar: Error is not recoverable: exiting now

Dockerfile:11

10 | WORKDIR /workspace/FunGAP/external/ 11 | >>> RUN tar -zxvf gmes_linux_64_4.tar.gz \ 12 | >>> && gunzip gm_key_64.gz \ 13 | >>> && cp gm_key_64 ~/.gm_key \ 14 | >>> && cd $FUNGAP_DIR/external/gmes_linux_64_4/ \ 15 | >>> && cp other/reformat_fasta.pl . \ 16 | >>> && perl change_path_in_perl_scripts.pl "/usr/bin/env perl" 17 |

ERROR: failed to solve: process "/bin/sh -c tar -zxvf gmes_linux_64_4.tar.gz && gunzip gm_key_64.gz && cp gm_key_64 ~/.gm_key && cd $FUNGAP_DIR/external/gmes_linux_64_4/ && cp other/reformat_fasta.pl . && perl change_path_in_perl_scripts.pl \"/usr/bin/env perl\"" did not complete successfully: exit code: 2

Can you please help me with this? Seems like the commands require the same file with two different names: gmes_linux_64_4.tar.gz and gmes_linux_64.tar.gz

mbnmbn00 commented 10 months ago

The file name that you need to download and provide is gmes_linux_64_4.tar.gz. GeneMark is protected by a license, although it's free for academic use. Therefore, users should download the program and provide it for the Docker installation. Please follow this instruction: https://github.com/CompSynBioLab-KoreaUniv/FunGAP/blob/master/docker/README.md

If you already provided the files, please let me know!

Debatosh commented 10 months ago

Thank you. Yes, I know that. I did download it and kept in the required folder to build docker image.

However if I am keeping gmes_linux_64_4.tar.gz, it is failing at an early stage that it cannot find gmes_linux_64.tar.gz, while if I keep gmes_linux_64.tar.gz in that folder, it is failing at a later stage. So both versions avialble for download are leading to errors at the different stages during docker image build process.

See this line from above log: CACHED [2/6] COPY gmes_linux_64.tar.gz /workspace/FunGAP/external/ 0.0s If I keep gmes_linux_64_4.tar.gz in the folder, this step fails. While if I keep the gmes_linux_64.tar.gz file instead, it is failing as shown above: 0.297 tar (child): gmes_linux_64_4.tar.gz: Cannot open: No such file or directory

It seems that both are needed in the docker image build process but it can use only one of them since if I keep both files int he folder even then it fails.

Can you check that only gmes_linux_64_4.tar.gz is needed and not the gmes_linux_64.tar.gz one?

Regards.

mbnmbn00 commented 10 months ago

Thanks. While I re-check the installation, can you show me the error message of later stage? It should be gmes_linux_64_4.tar.gz.

Debatosh commented 10 months ago

I am sorry but I was trying the Singularity method and accidently deleted the log files for the Docker ones.

Debatosh commented 10 months ago

Meanwhile, I have successfully tested the Singularity image based analysis on the test dataset of yeast. Can I contact you for suggestions on downstream analysis?

mbnmbn00 commented 10 months ago

Yeah, awesome! 😄 Shoot me an email, please!

Debatosh commented 10 months ago

Can I use this thread for asking queries?

On Fri, Dec 29, 2023 at 7:31 PM mbnmbn00 @.***> wrote:

Closed #99 https://github.com/CompSynBioLab-KoreaUniv/FunGAP/issues/99 as completed.

— Reply to this email directly, view it on GitHub https://github.com/CompSynBioLab-KoreaUniv/FunGAP/issues/99#event-11359178276, or unsubscribe https://github.com/notifications/unsubscribe-auth/AHD4DLYHBGHORYXT64NKAADYL5VHTAVCNFSM6AAAAABBF6AZBSVHI2DSMVQWIX3LMV45UABCJFZXG5LFIV3GK3TUJZXXI2LGNFRWC5DJN5XDWMJRGM2TSMJXHAZDONQ . You are receiving this because you authored the thread.Message ID: @.*** com>

-- Dr. Debatosh Das, ORISE Researcher, USDA-ARS Email: @.*** Skype: debatosh_das

mbnmbn00 commented 10 months ago

Oh, responding to that thread posts on GitHub (which is not private). My email address is here: https://github.com/CompSynBioLab-KoreaUniv/FunGAP?tab=readme-ov-file#contact