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View Code? Open in Web Editor NEWIntrome prioritises coding and noncoding splice-altering variants for clinical variant interpretation
License: GNU General Public License v3.0
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Unable to build MMSplice Docker container on M2 Mac
Hello,
I am encountering issues when building the MMSplice Docker container on an M2 Mac. As per the instructions in the GitHub, I have pulled MMSplice into the Introme folder, and have retained the original Dockerfile as specified here. When I attempt to build the container via docker build -t mmsplice ., I encounter the following error:
=> ERROR [ 6/18] RUN wget --quiet https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh -O ./miniconda.sh && /bin/bash ./miniconda.sh -b -p /opt/conda && rm ./miniconda.sh 14.4s
------
> [ 6/18] RUN wget --quiet https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh -O ./miniconda.sh && /bin/bash ./miniconda.sh -b -p /opt/conda && rm ./miniconda.sh:
13.59 PREFIX=/opt/conda
14.16 Unpacking payload ...
14.16 rosetta error: failed to open elf at /lib64/ld-linux-x86-64.so.2
14.16 ./miniconda.sh: line 442: 43 Exit 141 extract_range $boundary1 $boundary2
14.16 44 Trace/breakpoint trap | CONDA_QUIET="$BATCH" "$CONDA_EXEC" constructor --extract-tarball --prefix "$PREFIX"
------
3 warnings found (use --debug to expand):
- LegacyKeyValueFormat: "ENV key=value" should be used instead of legacy "ENV key value" format (line 5)
- LegacyKeyValueFormat: "ENV key=value" should be used instead of legacy "ENV key value" format (line 7)
- WorkdirRelativePath: Relative workdir "./mmsplice" can have unexpected results if the base image changes (line 31)
Dockerfile:16
--------------------
15 | # conda installation
16 | >>> RUN wget --quiet https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh -O ./miniconda.sh && \
17 | >>> /bin/bash ./miniconda.sh -b -p /opt/conda && \
18 | >>> rm ./miniconda.sh
19 |
--------------------
ERROR: failed to solve: process "/bin/sh -c wget --quiet https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh -O ./miniconda.sh && /bin/bash ./miniconda.sh -b -p /opt/conda && rm ./miniconda.sh" did not complete successfully: exit code: 133
Given this may originate from me using an M2 Mac, I did also attempt to build via docker build --platform linux/amd64 -t mmsplice ., however this returned an error relating to Python installation:
=> ERROR [ 7/18] RUN conda install python=3.6 8.3s
------
> [ 7/18] RUN conda install python=3.6:
1.359 Channels:
1.359 - defaults
1.359 Platform: linux-64
1.359 Collecting package metadata (repodata.json): ...working... done
4.892 Solving environment: ...working... failed
8.076
8.076 LibMambaUnsatisfiableError: Encountered problems while solving:
8.076 - package anaconda-anon-usage-0.4.0-py38hc06175d_0 requires python >=3.8,<3.9.0a0, but none of the providers can be installed
8.076
8.076 Could not solve for environment specs
8.076 The following packages are incompatible
8.076 ├─ anaconda-anon-usage is installable with the potential options
8.076 │ ├─ anaconda-anon-usage [0.2.0|0.3.0|...|0.4.4] would require
8.076 │ │ └─ python >=3.8,<3.9.0a0 , which can be installed;
8.076 │ ├─ anaconda-anon-usage [0.4.3|0.4.4] would require
8.076 │ │ └─ python >=3.12,<3.13.0a0 , which can be installed;
8.076 │ ├─ anaconda-anon-usage [0.2.0|0.3.0|...|0.4.4] would require
8.076 │ │ └─ python >=3.10,<3.11.0a0 , which can be installed;
8.076 │ ├─ anaconda-anon-usage [0.2.0|0.3.0|...|0.4.4] would require
8.076 │ │ └─ python >=3.11,<3.12.0a0 , which can be installed;
8.076 │ └─ anaconda-anon-usage [0.2.0|0.3.0|...|0.4.4] would require
8.076 │ └─ python >=3.9,<3.10.0a0 , which can be installed;
8.076 └─ python 3.6** is not installable because it conflicts with any installable versions previously reported.
8.076
------
3 warnings found (use --debug to expand):
- LegacyKeyValueFormat: "ENV key=value" should be used instead of legacy "ENV key value" format (line 5)
- LegacyKeyValueFormat: "ENV key=value" should be used instead of legacy "ENV key value" format (line 7)
- WorkdirRelativePath: Relative workdir "./mmsplice" can have unexpected results if the base image changes (line 31)
Dockerfile:21
--------------------
19 |
20 | # python pip updates
21 | >>> RUN conda install python=3.6
22 | RUN conda config --add channels bioconda
23 | RUN conda install cyvcf2 -y
--------------------
ERROR: failed to solve: process "/bin/sh -c conda install python=3.6" did not complete successfully: exit code: 1
It would seem there are issues with Conda and Python installation in the Dockerfile - however I am unsure what specific versions should be installed, or if I am approaching this the wrong way. Could you advise on how I should proceed with the installation?
Thanks,
Kevin
Issues getting SPIDEX v1.0 and dbscSNV v1.1
Hi,
I have some difficulties getting the depending annotation files for introme which are:
-
SPIDEX v1.0
-> https://www.openbioinformatics.org/annovar/spidex_download_form.php
I tried to gain access, but I didn't receive any reponse yet. -
dbscSNV 1.1
-> ftp://dbnsfp:[email protected]/dbscSNV1.1.zip
this does not seem to work/oudtaed?
help would be much appreciated, excited to install introme and try it out!
Best,
Andi
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