Singularity container for juicer and 3d-dna

[Michał T. Lorenc]

Hello,

Has anyone created a Singularity container for juicer and 3d-dna?

Thank you in advance,

Best wishes,

Michal

[Muhammad Saad Shamim]

There's a docker container, but I'm not aware of a singularity container.

- Muhammad Saad Shamim

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[Muhammad Saad Shamim]

Note that the docker container is currently for juicer.

If you're interested in making a singularity container for juicer/3d-dna, we're happy to help!

Best,

- Muhammad Saad Shamim

[Michał T. Lorenc]

Hi Muhammad,

Please find below a 3d-dna Singularity container:

BootStrap: docker

From: debian:stretch-backports

%help

  A container with 3d-dna

%post

  apt-get update && apt-get -y upgrade

  apt-get -y install \

    build-essential \

  wget \

  bzip2 \

  ca-certificates \

  libglib2.0-0 \

  libxext6 \

  libsm6 \

  libxrender1 \

  git 

  rm -rf /var/lib/apt/lists/*

  apt-get clean

  # download and install Miniconda

  echo 'export PATH=/opt/conda/bin:$PATH' > /etc/profile.d/conda.sh

  wget -c https://repo.continuum.io/miniconda/Miniconda2-latest-Linux-x86_64.sh

/bin/bash Miniconda2-latest-Linux-x86_64.sh -b -p /opt/conda

rm -rf Miniconda2-latest-Linux-x86_64.sh

  # add bioconda channels

  conda config --add channels defaults

  conda config --add channels conda-forge

  conda config --add channels bioconda

  conda update conda

  # install 3d-dna dependecies

  conda install lastz=1.0.4

  conda install openjdk=8.0.152 

  conda install gawk=4.2.1

  conda install coreutils=8.30

  conda install parallel=20180522

  conda install python=2.7

  conda install numpy=1.15.1

  conda install scipy=1.1.0

  conda install matplotlib=2.2.3

  # install 3d-dna

  git clone https://github.com/theaidenlab/3d-dna.git

%environment

  PATH=/opt/conda/bin:$PATH

Please let me know whether I got all depedencies with the right versions?

Thank you in advance.

Best wishes,

Michal

[Muhammad Saad Shamim]

Hey Michał!

I think the LastZ version needs to be newer? 

3d-dna used 1.03.73 but the singularity container is using 1.0.4 (unless they changed numbering system perhaps)?

The rest of the dependencies seem ok.

- Muhammad Saad Shamim

To view this discussion on the web visit https://groups.google.com/d/msgid/3d-genomics/89eaa1a3-7b73-448c-b69c-c91bcc3b7965%40googlegroups.com.

[Michał T. Lorenc]

Hi Muhammad,
I can not find lastz 1.03.73 version. Could you please provide me a link to it?

Thank you in advance,

Michal

On 9/16/18, Muhammad Saad Shamim <sa50...@gmail.com> wrote:
> Hey Michał!
>
> I think the LastZ version needs to be newer?
> 3d-dna used 1.03.73 but the singularity container is using 1.0.4 (unless
> they changed numbering system perhaps)?
> The rest of the dependencies seem ok.
>

> - Muhammad Saad Shamim <http://mshamim.com/>

>
>
> On Sun, Sep 9, 2018 at 11:47 PM Michał T. Lorenc <m.t.l...@gmail.com>
> wrote:
>
>> Hi Muhammad,
>> Please find below a 3d-dna Singularity container:
>>

>> *BootStrap: docker*
>> *From: debian:stretch-backports*
>>
>> *%help*
>> * A container with 3d-dna*
>>
>> *%post*
>> * apt-get update && apt-get -y upgrade*
>> * apt-get -y install \*
>> * build-essential \*
>> * wget \*
>> * bzip2 \*
>> * ca-certificates \*
>> * libglib2.0-0 \*
>> * libxext6 \*
>> * libsm6 \*
>> * libxrender1 \*
>> * git *
>>
>> * rm -rf /var/lib/apt/lists/**
>> * apt-get clean*
>>
>> * # download and install Miniconda*
>> * echo 'export PATH=/opt/conda/bin:$PATH' > /etc/profile.d/conda.sh*
>> * wget -c
>> https://repo.continuum.io/miniconda/Miniconda2-latest-Linux-x86_64.sh
>> <https://repo.continuum.io/miniconda/Miniconda2-latest-Linux-x86_64.sh>*
>> * /bin/bash Miniconda2-latest-Linux-x86_64.sh -b -p /opt/conda*
>> * rm -rf Miniconda2-latest-Linux-x86_64.sh*
>>
>> * # add bioconda channels*
>> * conda config --add channels defaults*
>> * conda config --add channels conda-forge*
>> * conda config --add channels bioconda*
>> * conda update conda*
>>
>> * # install 3d-dna dependecies*
>> * conda install lastz=1.0.4*
>> * conda install openjdk=8.0.152 *
>> * conda install gawk=4.2.1*
>> * conda install coreutils=8.30*
>> * conda install parallel=20180522*
>> * conda install python=2.7*
>> * conda install numpy=1.15.1*
>> * conda install scipy=1.1.0*
>> * conda install matplotlib=2.2.3*
>>
>> * # install 3d-dna*
>> * git clone https://github.com/theaidenlab/3d-dna.git
>> <https://github.com/theaidenlab/3d-dna.git>*
>>
>> *%environment*
>> * PATH=/opt/conda/bin:$PAT*H

>>
>>
>> Please let me know whether I got all depedencies with the right versions?
>>
>> Thank you in advance.
>>
>> Best wishes,
>>
>> Michal
>>
>> On Friday, September 7, 2018 at 2:48:02 PM UTC+10, Muhammad Shamim wrote:
>>>
>>> Note that the docker container is currently for juicer.
>>> If you're interested in making a singularity container for
>>> juicer/3d-dna,
>>> we're happy to help!
>>>
>>> Best,

>>> - Muhammad Saad Shamim <http://mshamim.com/>

>>>
>>>
>>> On Thu, Sep 6, 2018 at 11:16 PM Muhammad Saad Shamim <sa50...@gmail.com>
>>> wrote:
>>>
>>>> There's a docker container, but I'm not aware of a singularity
>>>> container.
>>>>

>>>> - Muhammad Saad Shamim <http://mshamim.com/>

>>>>
>>>>
>>>> On Thu, Sep 6, 2018 at 10:52 PM Michał T. Lorenc <m.t.l...@gmail.com>
>>>> wrote:
>>>>
>>>>> Hello,
>>>>> Has anyone created a Singularity

>>>>> <https://docs.hpc.arizona.edu/display/UAHPC/Singularity+Tutorials>

>>>>> container for juicer and 3d-dna?
>>>>>
>>>>> Thank you in advance,
>>>>>
>>>>> Best wishes,
>>>>>
>>>>> Michal
>>>>>
>>>>>
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>>>>>
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>> <https://groups.google.com/d/msgid/3d-genomics/89eaa1a3-7b73-448c-b69c-c91bcc3b7965%40googlegroups.com?utm_medium=email&utm_source=footer>
>> .

[Muhammad Shamim]

Sure, I think it's this http://www.bx.psu.edu/~rsharris/lastz/newer/README.lastz-1.03.73.html

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