Local conda recipe mulled container build fails with HTTP error for local files

[pcm32]

On macOS High Sierra, executing:

mulled-build build-and-test 'r-seurat-workflow=0.0.1--0' --extra-channel file://Users/pmoreno/miniconda3/conda-bld/ --test 'which read-10x.R' --involucro-path /Users/pmoreno/venvs/mulled/bin/involucro

fails with:

/Users/pmoreno/venvs/mulled/bin/involucro -v=2 -f /Users/pmoreno/venvs/mulled/lib/python2.7/site-packages/galaxy/tools/deps/mulled/invfile.lua -set CHANNELS='bioconda,file://Users/pmoreno/miniconda3/conda-bld/' -set TEST='which read-10x.R' -set TARGETS='r-seurat-workflow=0.0.1=0' -set REPO='quay.io/biocontainers/r-seurat-workflow:0.0.1--0' -set BINDS='build/dist:/usr/local/,/Users/pmoreno/miniconda3/conda-bld/:/Users/pmoreno/miniconda3/conda-bld/' build-and-test
.No handlers could be found for logger "galaxy.tools.deps.commands"
[Jul  4 11:48:46] DEBU Run file [/Users/pmoreno/venvs/mulled/lib/python2.7/site-packages/galaxy/tools/deps/mulled/invfile.lua]
[Jul  4 11:48:46] INFO Invoke Task [build]
[Jul  4 11:48:46] STEP Run image [continuumio/miniconda3:latest] with command [[rm -rf /data/dist]]
[Jul  4 11:48:46] DEBU Creating container [step-d2ac29a445]
[Jul  4 11:48:46] DEBU Image [continuumio/miniconda3:latest] not present, pulling it
[Jul  4 11:48:46] DEBU Pull Image [continuumio/miniconda3:latest]
[Jul  4 11:49:07] DEBU Created container [9dd653a644bf step-d2ac29a445], starting it
[Jul  4 11:49:07] DEBU Container [9dd653a644bf step-d2ac29a445] started, waiting for completion
[Jul  4 11:49:08] DEBU Container [9dd653a644bf step-d2ac29a445] completed with exit code [0] as expected
[Jul  4 11:49:08] DEBU Container [9dd653a644bf step-d2ac29a445] removed
[Jul  4 11:49:08] STEP Run image [continuumio/miniconda3:latest] with command [[/bin/sh -c conda install  -c bioconda -c file://Users/pmoreno/miniconda3/conda-bld/  r-seurat-workflow=0.0.1=0 -p /usr/local --copy --yes --quiet]]
[Jul  4 11:49:08] DEBU Creating container [step-8f97df74f8]
[Jul  4 11:49:08] DEBU Created container [9fa5aa8d945d step-8f97df74f8], starting it
[Jul  4 11:49:09] DEBU Container [9fa5aa8d945d step-8f97df74f8] started, waiting for completion
[Jul  4 11:49:09] SOUT Solving environment: ...working... failed
[Jul  4 11:49:10] SERR 
[Jul  4 11:49:10] SERR # >>>>>>>>>>>>>>>>>>>>>> ERROR REPORT <<<<<<<<<<<<<<<<<<<<<<
[Jul  4 11:49:10] SERR 
[Jul  4 11:49:10] SERR `$ /opt/conda/bin/conda install -c bioconda -c file://Users/pmoreno/miniconda3/conda-bld/ r-seurat-workflow=0.0.1=0 -p /usr/local --copy --yes --quiet`
[Jul  4 11:49:10] SERR 
[Jul  4 11:49:10] SERR environment variables:
[Jul  4 11:49:10] SERR CIO_TEST=<not set>
[Jul  4 11:49:10] SERR CONDA_ROOT=/opt/conda
[Jul  4 11:49:10] SERR PATH=/opt/conda/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin
[Jul  4 11:49:10] SERR :/bin
[Jul  4 11:49:10] SERR REQUESTS_CA_BUNDLE=<not set>
[Jul  4 11:49:10] SERR SSL_CERT_FILE=<not set>
[Jul  4 11:49:10] SERR 
[Jul  4 11:49:10] SERR active environment : None
[Jul  4 11:49:10] SERR user config file : /root/.condarc
[Jul  4 11:49:10] SERR populated config files :
[Jul  4 11:49:10] SERR conda version : 4.5.4
[Jul  4 11:49:10] SERR conda-build version : not installed
[Jul  4 11:49:10] SERR python version : 3.6.5.final.0
[Jul  4 11:49:10] SERR base environment : /opt/conda  (writable)
[Jul  4 11:49:10] SERR channel URLs : https://conda.anaconda.org/bioconda/linux-64
[Jul  4 11:49:10] SERR https://conda.anaconda.org/bioconda/noarch
[Jul  4 11:49:10] SERR file://users/pmoreno/miniconda3/conda-bld/linux-64
[Jul  4 11:49:10] SERR file://users/pmoreno/miniconda3/conda-bld/noarch
[Jul  4 11:49:10] SERR https://repo.anaconda.com/pkgs/main/linux-64
[Jul  4 11:49:10] SERR https://repo.anaconda.com/pkgs/main/noarch
[Jul  4 11:49:10] SERR https://repo.anaconda.com/pkgs/free/linux-64
[Jul  4 11:49:10] SERR https://repo.anaconda.com/pkgs/free/noarch
[Jul  4 11:49:10] SERR https://repo.anaconda.com/pkgs/r/linux-64
[Jul  4 11:49:10] SERR https://repo.anaconda.com/pkgs/r/noarch
[Jul  4 11:49:10] SERR https://repo.anaconda.com/pkgs/pro/linux-64
[Jul  4 11:49:10] SERR https://repo.anaconda.com/pkgs/pro/noarch
[Jul  4 11:49:10] SERR package cache : /opt/conda/pkgs
[Jul  4 11:49:10] SERR /root/.conda/pkgs
[Jul  4 11:49:10] SERR envs directories : /opt/conda/envs
[Jul  4 11:49:10] SERR /root/.conda/envs
[Jul  4 11:49:10] SERR platform : linux-64
[Jul  4 11:49:10] SERR user-agent : conda/4.5.4 requests/2.18.4 CPython/3.6.5 Linux/4.9.87-linuxkit-aufs debian/9 glibc/2.24
[Jul  4 11:49:10] SERR UID:GID : 0:0
[Jul  4 11:49:10] SERR netrc file : None
[Jul  4 11:49:10] SERR offline mode : False
[Jul  4 11:49:10] SERR 
[Jul  4 11:49:10] SERR 
[Jul  4 11:49:10] SERR V V V V V V V V V V V V V V V V V V V V V V V V V V V V V V V
[Jul  4 11:49:10] SERR 
[Jul  4 11:49:10] SERR CondaHTTPError: HTTP 404 CONNECTION FAILED for url <file://users/pmoreno/miniconda3/conda-bld/noarch/repodata.json>
[Jul  4 11:49:10] SERR Elapsed: 00:00.000194
[Jul  4 11:49:10] SERR 
[Jul  4 11:49:10] SERR The remote server could not find the noarch directory for the
[Jul  4 11:49:10] SERR requested channel with url: file://users/pmoreno/miniconda3/conda-bld
[Jul  4 11:49:10] SERR 
[Jul  4 11:49:10] SERR As of conda 4.3, a valid channel must contain a `noarch/repodata.json` and
[Jul  4 11:49:10] SERR associated `noarch/repodata.json.bz2` file, even if `noarch/repodata.json` is
[Jul  4 11:49:10] SERR empty. please request that the channel administrator create
[Jul  4 11:49:10] SERR `noarch/repodata.json` and associated `noarch/repodata.json.bz2` files.
[Jul  4 11:49:10] SERR $ mkdir noarch
[Jul  4 11:49:10] SERR $ echo '{}' > noarch/repodata.json
[Jul  4 11:49:10] SERR $ bzip2 -k noarch/repodata.json
[Jul  4 11:49:10] SERR 
[Jul  4 11:49:10] SERR You will need to adjust your conda configuration to proceed.
[Jul  4 11:49:10] SERR Use `conda config --show channels` to view your configuration's current state.
[Jul  4 11:49:10] SERR Further configuration help can be found at <https://conda.io/docs/config.html>.
[Jul  4 11:49:10] SERR 
[Jul  4 11:49:10] SERR A reportable application error has occurred. Conda has prepared the above report.
[Jul  4 11:49:10] SERR Upload successful.
[Jul  4 11:49:11] ERRO Task processing failed: Unexpected exit code [1] of container [9fa5aa8d945d step-8f97df74f8], container preserved

Main error seems to be:

[Jul  4 11:49:10] SERR CondaHTTPError: HTTP 404 CONNECTION FAILED for url <file://users/pmoreno/miniconda3/conda-bld/noarch/repodata.json>

although the file does exist in the host file system:

ls -l ~/miniconda3/conda-bld/noarch/repodata.json
-rw-r--r--  1 pmoreno  staff  61  4 Jul 10:17 /Users/pmoreno/miniconda3/conda-bld/noarch/repodata.json

I presume that there must be an option to add certain directories to the container that I'm missing. I had previously indexed the local channel as suggested here.

Thanks!

[bgruening]

Have you indexed /Users/pmoreno/miniconda3/conda-bld/ or /Users/pmoreno/miniconda3/conda-bld/linux-64/?

[pcm32]

Yes I did.... My impression is that this is running inside a container or something as it is claiming that conda is being used from a different path to where conda is on Mac; maybe then the /Users/my-user dir is not being mounted inside that container?

[bgruening]

Urg, OSX. I have no clue how this works :(
I will try to find a Mac tomorrow, sorry.