Problem building Dockerfile.base

[pvilaca]

Hi

I am trying to run the Selenzime in my local machine but I am not able to build the Dockerfile.base.

It seems dependencies problems...
Can someone help me?

Command with problems

docker build -t sbc/selenzybase -f Dockerfile.base .

Output

Step 1/2 : FROM continuumio/anaconda3:5.2.0
 ---> 61836e3344e7
Step 2/2 : RUN conda install -c conda-forge flask-restful=0.3.6 --no-update-dependencies   && conda install -c bioconda emboss=6.5.7   && conda install -c rdkit rdkit=2017.09.3.0   && conda install -c anaconda biopython=1.69   && conda install -c biobuilds t-coffee=11.00
 ---> Running in c058321ff225
Solving environment: ...working... done

## Package Plan ##

  environment location: /opt/conda

  added / updated specs: 
    - flask-restful=0.3.6


The following packages will be downloaded:

    package                    |            build
    ---------------------------|-----------------
    aniso8601-8.0.0            |             py_0          32 KB  conda-forge
    sqlite-3.28.0              |       h8b20d00_0         1.9 MB  conda-forge
    python_abi-3.7             |          1_cp37m           4 KB  conda-forge
    pytz-2020.1                |     pyh9f0ad1d_0         227 KB  conda-forge
    setuptools-46.1.3          |   py37hc8dfbb8_0         634 KB  conda-forge
    werkzeug-1.0.1             |     pyh9f0ad1d_0         239 KB  conda-forge
    ca-certificates-2020.4.5.1 |       hecc5488_0         146 KB  conda-forge
    bzip2-1.0.8                |       h516909a_2         396 KB  conda-forge
    ncurses-6.1                |       hfc679d8_2         1.3 MB  conda-forge
    python-dateutil-2.8.1      |             py_0         220 KB  conda-forge
    jinja2-2.11.2              |     pyh9f0ad1d_0          93 KB  conda-forge
    certifi-2020.4.5.1         |   py37hc8dfbb8_0         151 KB  conda-forge
    python-3.7.1               |       h5001a0f_0        26.8 MB  conda-forge
    flask-1.1.2                |     pyh9f0ad1d_0          70 KB  conda-forge
    tk-8.6.10                  |       hed695b0_0         3.2 MB  conda-forge
    xz-5.2.5                   |       h516909a_0         430 KB  conda-forge
    _libgcc_mutex-0.1          |      conda_forge           3 KB  conda-forge
    openssl-1.0.2u             |       h516909a_0         3.2 MB  conda-forge
    libgomp-9.2.0              |       h24d8f2e_2         816 KB  conda-forge
    libgcc-ng-9.2.0            |       h24d8f2e_2         8.2 MB  conda-forge
    zlib-1.2.11                |    h516909a_1006         105 KB  conda-forge
    readline-7.0               |    hf8c457e_1001         391 KB  conda-forge
    wheel-0.34.2               |             py_1          24 KB  conda-forge
    _openmp_mutex-4.5          |            0_gnu         435 KB  conda-forge
    libffi-3.2.1               |       hfc679d8_5          51 KB  conda-forge
    pip-20.1                   |     pyh9f0ad1d_0         1.1 MB  conda-forge
    flask-restful-0.3.6        |             py_1          22 KB  conda-forge
    markupsafe-1.1.1           |   py37h8f50634_1          26 KB  conda-forge
    click-7.1.2                |     pyh9f0ad1d_0          64 KB  conda-forge
    six-1.14.0                 |             py_1          13 KB  conda-forge
    itsdangerous-1.1.0         |             py_0          16 KB  conda-forge
    pycrypto-2.6.1             |py37h8f50634_1004         472 KB  conda-forge
    ------------------------------------------------------------
                                           Total:        50.6 MB

The following NEW packages will be INSTALLED:

    _libgcc_mutex:   0.1-conda_forge       conda-forge
    _openmp_mutex:   4.5-0_gnu             conda-forge
    aniso8601:       8.0.0-py_0            conda-forge
    flask-restful:   0.3.6-py_1            conda-forge
    libgomp:         9.2.0-h24d8f2e_2      conda-forge
    python_abi:      3.7-1_cp37m           conda-forge

The following packages will be UPDATED:

    bzip2:           1.0.6-h14c3975_5                  --> 1.0.8-h516909a_2          conda-forge
    ca-certificates: 2018.03.07-0                      --> 2020.4.5.1-hecc5488_0     conda-forge
    certifi:         2018.4.16-py36_0                  --> 2020.4.5.1-py37hc8dfbb8_0 conda-forge
    click:           6.7-py36h5253387_0                --> 7.1.2-pyh9f0ad1d_0        conda-forge
    flask:           1.0.2-py36_1                      --> 1.1.2-pyh9f0ad1d_0        conda-forge
    itsdangerous:    0.24-py36h93cc618_1               --> 1.1.0-py_0                conda-forge
    jinja2:          2.10-py36ha16c418_0               --> 2.11.2-pyh9f0ad1d_0       conda-forge
    libffi:          3.2.1-hd88cf55_4                  --> 3.2.1-hfc679d8_5          conda-forge
    libgcc-ng:       7.2.0-hdf63c60_3                  --> 9.2.0-h24d8f2e_2          conda-forge
    markupsafe:      1.0-py36hd9260cd_1                --> 1.1.1-py37h8f50634_1      conda-forge
    ncurses:         6.1-hf484d3e_0                    --> 6.1-hfc679d8_2            conda-forge
    openssl:         1.0.2o-h20670df_0                 --> 1.0.2u-h516909a_0         conda-forge
    pip:             10.0.1-py36_0                     --> 20.1-pyh9f0ad1d_0         conda-forge
    pycrypto:        2.6.1-py36h14c3975_8              --> 2.6.1-py37h8f50634_1004   conda-forge
    python:          3.6.5-hc3d631a_2                  --> 3.7.1-h5001a0f_0          conda-forge
    python-dateutil: 2.7.3-py36_0                      --> 2.8.1-py_0                conda-forge
    pytz:            2018.4-py36_0                     --> 2020.1-pyh9f0ad1d_0       conda-forge
    readline:        7.0-ha6073c6_4                    --> 7.0-hf8c457e_1001         conda-forge
    setuptools:      39.1.0-py36_0                     --> 46.1.3-py37hc8dfbb8_0     conda-forge
    six:             1.11.0-py36h372c433_1             --> 1.14.0-py_1               conda-forge
    sqlite:          3.23.1-he433501_0                 --> 3.28.0-h8b20d00_0         conda-forge
    tk:              8.6.7-hc745277_3                  --> 8.6.10-hed695b0_0         conda-forge
    werkzeug:        0.14.1-py36_0                     --> 1.0.1-pyh9f0ad1d_0        conda-forge
    wheel:           0.31.1-py36_0                     --> 0.34.2-py_1               conda-forge
    xz:              5.2.4-h14c3975_4                  --> 5.2.5-h516909a_0          conda-forge
    zlib:            1.2.11-ha838bed_2                 --> 1.2.11-h516909a_1006      conda-forge

Proceed ([y]/n)? 


==> WARNING: A newer version of conda exists. <==
  current version: 4.5.4
  latest version: 4.8.3

Please update conda by running

    $ conda update -n base conda


aniso8601-8.0.0      |   32 KB | ########## | 100% 
sqlite-3.28.0        |  1.9 MB | ########## | 100% 
python_abi-3.7       |    4 KB | ########## | 100% 
pytz-2020.1          |  227 KB | ########## | 100% 
setuptools-46.1.3    |  634 KB | ########## | 100% 
werkzeug-1.0.1       |  239 KB | ########## | 100% 
ca-certificates-2020 |  146 KB | ########## | 100% 
bzip2-1.0.8          |  396 KB | ########## | 100% 
ncurses-6.1          |  1.3 MB | ########## | 100% 
python-dateutil-2.8. |  220 KB | ########## | 100% 
jinja2-2.11.2        |   93 KB | ########## | 100% 
certifi-2020.4.5.1   |  151 KB | ########## | 100% 
python-3.7.1         | 26.8 MB | ########## | 100% 
flask-1.1.2          |   70 KB | ########## | 100% 
tk-8.6.10            |  3.2 MB | ########## | 100% 
xz-5.2.5             |  430 KB | ########## | 100% 
_libgcc_mutex-0.1    |    3 KB | ########## | 100% 
openssl-1.0.2u       |  3.2 MB | ########## | 100% 
libgomp-9.2.0        |  816 KB | ########## | 100% 
libgcc-ng-9.2.0      |  8.2 MB | ########## | 100% 
zlib-1.2.11          |  105 KB | ########## | 100% 
readline-7.0         |  391 KB | ########## | 100% 
wheel-0.34.2         |   24 KB | ########## | 100% 
_openmp_mutex-4.5    |  435 KB | ########## | 100% 
libffi-3.2.1         |   51 KB | ########## | 100% 
pip-20.1             |  1.1 MB | ########## | 100% 
flask-restful-0.3.6  |   22 KB | ########## | 100% 
markupsafe-1.1.1     |   26 KB | ########## | 100% 
click-7.1.2          |   64 KB | ########## | 100% 
six-1.14.0           |   13 KB | ########## | 100% 
itsdangerous-1.1.0   |   16 KB | ########## | 100% 
pycrypto-2.6.1       |  472 KB | ########## | 100% 
Downloading and Extracting Packages
Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... failed

ERROR conda.core.link:_execute(502): An error occurred while installing package 'conda-forge::click-7.1.2-pyh9f0ad1d_0'.
FileNotFoundError(2, "No such file or directory: '/opt/conda/bin/python3.7'")
Attempting to roll back.

Rolling back transaction: ...working... done

FileNotFoundError(2, "No such file or directory: '/opt/conda/bin/python3.7'")


The command '/bin/sh -c conda install -c conda-forge flask-restful=0.3.6 --no-update-dependencies   && conda install -c bioconda emboss=6.5.7   && conda install -c rdkit rdkit=2017.09.3.0   && conda install -c anaconda biopython=1.69   && conda install -c biobuilds t-coffee=11.00' returned a non-zero code: 1

[RuthStoney]

Hi,

My first suggestion would be checking that you have sqlite3 installed on your computer.

If that doesn't fix it then try making the following alterations to the Dockerfile.base (just changing the order of installations and using a newer biopython fixed it for me):

Installtool: emboss=5.5.7s

RUN conda install -c bioconda emboss=6.5.7
&& conda install -c rdkit rdkit=2017.09.3.0
&& conda install -c conda-forge biopython=1.76
&& conda install -c biobuilds t-coffee=11.00
&& conda install -c conda-forge flask-restful=0.3.6

Please could you let me know if this solved the issues?
Thanks,
Ruth

[pvilaca]

Thank you @RuthStoney. It's working

I also had to change the version of anaconda base docker.

# Docker file that installs docker container for Selenzyme
#
# build with: "sudo docker build -t selenzyme ." 
FROM continuumio/anaconda3:5.0.1

 # Installtool: emboss=5.5.7s
RUN conda install -c conda-forge flask-restful=0.3.6 --no-update-dependencies \
  && conda install -c bioconda emboss=6.5.7 \
  && conda install -c rdkit rdkit=2017.09.3.0 \
  && conda install -c anaconda biopython=1.76 \
  && conda install -c biobuilds t-coffee=11.00