Closed sandbardev closed 5 years ago
Acribbs
commented
5 years ago Hi,
We have not tested the installation script on this version of Linux and it’s not clear from the log report what the obvious issue is. My first thought was that your LD_LIBRARY_PATH wasn’t set correctly but it seems as though it is.
Could you try installing the —production version of the code using the install script.
Alternatively, could you try conda install cgat-scripts to install the code.
sandbardev
commented
5 years ago Conda install does not seem to find the cgat-scripts packages. I tried
conda install cgat-scripts
as well as the the specific command on https://anaconda.org/bioconda/cgat-scripts
conda install -c bioconda cgat-scripts
and it resulted in
(cgat-scripts[v0.3.2]) sand@aspire-E5-571 ~ $ conda install -c bioconda cgat-scripts Solving environment: failed
PackagesNotFoundError: The following packages are not available from current channels:
- cgat-scripts
- python-lzo=1.11
- cgat-scripts
- bioconductor-ihw==1.2.0
- r-fdrtool
- cgat-scripts
- ggplot==0.6.8
- brewer2mpl
Current channels:
- https://conda.anaconda.org/bioconda/linux-64
- https://conda.anaconda.org/bioconda/noarch
- https://repo.anaconda.com/pkgs/main/linux-64
- https://repo.anaconda.com/pkgs/main/noarch
- https://repo.anaconda.com/pkgs/free/linux-64
- https://repo.anaconda.com/pkgs/free/noarch
- https://repo.anaconda.com/pkgs/r/linux-64
- https://repo.anaconda.com/pkgs/r/noarch
- https://repo.anaconda.com/pkgs/pro/linux-64
- https://repo.anaconda.com/pkgs/pro/noarch
To search for alternate channels that may provide the conda package you're looking for, navigate to
and use the search bar at the top of the page.
Am I missing any repositories here? I also tried running the script with the --production parameter to which it yielded this:
Installed /home/sand/cgat-install/cgat-apps Processing dependencies for cgat==0.5.3 Finished processing dependencies for cgat==0.5.3 Traceback (most recent call last): File "scripts/conda.py", line 47, in
(out, err) = run_command(statement) File "scripts/conda.py", line 41, in run_command raise Exception(issue) Exception: Problem running command: conda info --json Stderr was: b'/bin/bash: /home/sand/cgat-install/conda-install/envs/cgat-a/lib/libtinfo.so.5: no version >information available (required by /bin/bash)\n' ##########################################################
An error occurred in:
- line number: 418
- exit status: 1
- command: python scripts/conda.py
The script will abort now. User input was:
./install.sh --production
Please copy and paste this error and report it via Git Hub: https://github.com/cgat-developers/cgat-apps/issues
Debugging: CFLAGS: -I/home/sand/cgat-install/conda-install/envs/cgat-a/include -L/home/sand/cgat-install/conda-install/envs/cgat-a/lib CPATH: -I/home/sand/cgat-install/conda-install/envs/cgat-a/include -L/home/sand/cgat-install/conda-install/envs/cgat-a/lib C_INCLUDE_PATH: :/home/sand/cgat-install/conda-install/envs/cgat-a/include CPLUS_INCLUDE_PATH: :/home/sand/cgat-install/conda-install/envs/cgat-a/include LIBRARY_PATH: :/home/sand/cgat-install/conda-install/envs/cgat-a/lib LD_LIBRARY_PATH: :/home/sand/cgat-install/conda-install/envs/cgat-a/lib:/home/sand/cgat-install/conda-install/envs/cgat-a/lib/R/lib CGAT_HOME: /home/sand/cgat-install CONDA_INSTALL_DIR: /home/sand/cgat-install/conda-install CONDA_INSTALL_TYPE_APPS: apps-production.yml CONDA_INSTALL_TYPE_CORE: core-production.yml CONDA_INSTALL_ENV: cgat-a PYTHONPATH: INSTALL_BRANCH: master CORE_BRANCH: master RELEASE: CODE_DOWNLOAD_TYPE: 0
##########################################################
Acribbs
commented
5 years ago Hmm, i have just tested the installation on OSX and redhat luinx and all seems to work well. Can you run the command:
conda config --show-sources
and
conda config --show
Also, did you install using a clean environment?
Thanks
sandbardev
commented
5 years ago Yes, I did install using a clean environment. Interestingly, I exclusively managed to install the last repository(CGATOxford) in an OS identical to this one, which if exactly why I insisted on using Linux Mint 18.3 for this. Anyway, the output for the commands is as follows:
(cgat-apps) sand@aspire-E5-571 ~ $ conda config --show-sources
(cgat-apps) sand@aspire-E5-571 ~ $ conda config --show add_anaconda_token: True add_pip_as_python_dependency: True aggressive_update_packages:
- ca-certificates
- certifi
- openssl allow_non_channel_urls: False allow_softlinks: False always_copy: False always_softlink: False always_yes: None anaconda_upload: None auto_update_conda: True changeps1: True channel_alias: https://conda.anaconda.org channel_priority: True channels:
- defaults client_ssl_cert: None client_ssl_cert_key: None clobber: False create_default_packages: [] custom_channels: pkgs/main: https://repo.anaconda.com pkgs/free: https://repo.anaconda.com pkgs/r: https://repo.anaconda.com pkgs/pro: https://repo.anaconda.com custom_multichannels: defaults: ["https://repo.anaconda.com/pkgs/main", "https://repo.anaconda.com/pkgs/free", >"https://repo.anaconda.com/pkgs/r", "https://repo.anaconda.com/pkgs/pro"] local: [] default_channels:
- https://repo.anaconda.com/pkgs/main
- https://repo.anaconda.com/pkgs/free
- https://repo.anaconda.com/pkgs/r
- https://repo.anaconda.com/pkgs/pro disallowed_packages: [] download_only: False envs_dirs:
- /home/sand/.conda/envs
- /home/sand/miniconda3/envs force: False json: False local_repodata_ttl: 1 max_shlvl: 2 migrated_channel_aliases: [] no_dependencies: False non_admin_enabled: True notify_outdated_conda: True offline: False override_channels_enabled: True path_conflict: clobber pinned_packages: [] pkgs_dirs:
- /home/sand/miniconda3/pkgs
- /home/sand/.conda/pkgs proxy_servers: {} quiet: False remote_connect_timeout_secs: 9.15 remote_max_retries: 3 remote_read_timeout_secs: 60.0 report_errors: None rollback_enabled: True safety_checks: warn shortcuts: True show_channel_urls: None ssl_verify: True track_features: [] use_index_cache: False use_pip: True verbosity: 0 whitelist_channels: [] (cgat-apps) sand@aspire-E5-571 ~ $
I never needed to specifically add any external sources to perform conda installations, which I assume is why the output for the first command is empty.
sebastian-luna-valero
commented
5 years ago Hi,
The problem seems to occur when pinning the environment: https://github.com/cgat-developers/cgat-apps/blob/master/install.sh#L417
That wasn't performed in the CGATOxford installation.
Now that we have moved cgat-apps to bioconda:
http://bioconda.github.io/recipes/cgat-apps/README.html
Can I suggest that you try that instead, please?
Best regards, Sebastian
sebastian-luna-valero
commented
5 years ago Please re-open if needed.
Currently running Linux Mint 18.3 on XFCE. I believe the error message is self-explanatory.