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cnobles / iGUIDE

Bioinformatic pipeline for identifying dsDNA breaks by marker based incorporation, such as breaks induced by designer nucleases like Cas9.
https://iguide.readthedocs.io/en/latest/
GNU General Public License v3.0
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Issues creating and detecting the the iguide environment #70

Open pmendez00 opened 4 years ago

pmendez00 commented 4 years ago

Hi Christopher,

Thanks for putting iGUIDE together. This is great. While trying to install it has some issues creating the 'iguide' environment. See the screenshot attached. I'm looking forward to giving it a try this week and I would appreciate very much if you could help me out.

Thanks in advance for your time and help!!

Best regards,

Pedro Mendez.

iGUIDE_install_screenshot_Pedro_Mendez

cnobles commented 4 years ago

Hi Pedro,

Thanks for checking out iGUIDE, it's been a lot of fun to put together and I still hope to add some improvements on it.

I'm having issues recreating your issue though. Could you check to see which version of conda you are running? From the verbose installation, it looks like you already had miniconda installed.

I find it easiest to clone iGUIDE into my home directory and then setup up everything from there, rather than a temp directory.

Seeing that miniconda is installed on your system at root level, you may need to get your sys admin to update if that is a problem, or you could have them run the install of iguide and see if that works out.

I've retriggered the automated testing for iGUIDE through CircleCI and also ran it myself on the system used to develop the software, but I couldn't recreate your errors. Neither showed any issues with the installation.

Could you let me know a bit more about what your system is like or your goals of running iGUIDE?

Best, Chris

image

pmendez00 commented 4 years ago

Hi Chris,

Thanks a lot for getting back to us. I'll try to clone it first and install it from there. Also will double-check with our IT team to make sure that there isn't any incompatibility related to that too. I'll test it ASAP and will get back to you soon.

Again, thanks a lot for your support!

Have a great week ahead!!

Best,

Pedro.

This e-mail is privileged, confidential and contains private information. Any reading, retention, distribution or copy of this communication by any person other than its intended recipient is prohibited.

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On Mon, Jun 1, 2020 at 7:32 AM Chris Nobles notifications@github.com wrote:

Hi Pedro,

Thanks for checking out iGUIDE, it's been a lot of fun to put together and I still hope to add some improvements on it.

I'm having issues recreating your issue though. Could you check to see which version of conda you are running? From the verbose installation, it looks like you already had miniconda installed.

I find it easiest to clone iGUIDE into my home directory and then setup up everything from there, rather than a temp directory.

Seeing that miniconda is installed on your system at root level, you may need to get your sys admin to update if that is a problem, or you could have them run the install of iguide and see if that works out.

I've retriggered the automated testing for iGUIDE through CircleCI and also ran it myself on the system used to develop the software, but I couldn't recreate your errors. Neither showed any issues with the installation.

Could you let me know a bit more about what your system is like or your goals of running iGUIDE?

Best, Chris

[image: image] https://user-images.githubusercontent.com/12237291/83419319-e6ee2000-a3f2-11ea-8109-215232314dd6.png

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guygozlan commented 4 years ago

Hi iGuide team,

I am facing a similar issue. Trying to clone the repository again from the home directory did not help.

Note that I have anaconda3 installed in addition to the miniconda3. Should it be a problem?

Would really appreciate your help.

Thank you in advanced, Guy

image

cnobles commented 4 years ago

Hi Guy,

Could you post the results from running the install script with the "-v" flag, this should help in debugging. Seems like there may be some conflict if you have both installed (miniconda and anaconda). If that is an issue, then we could likely just do the install in a more manual fashion, but run it through anaconda.

A manual setup may be helpful if this turns out to be a reoccurring issue.

Best, Chris

guygozlan commented 4 years ago

Hi Chris, Thank you so much for your quick reply. Please see the screenshot from running with "-v" flag. If there is a way to do manual setup - it could be very helpful. Thank you, Guy

image

cnobles commented 4 years ago

Alright, let's try an manual install. I should likely update the docs with this process as well. If it's not clear, anything in the code blocks should be input into the command line. My preferred installation has both the miniconda and iGUIDE directories in my home directory.

Installing miniconda

Skip to installing iGUIDE if you already have miniconda or anaconda installed. These can be executed in your home directory.

  1. Get the latest version of miniconda install script.
__conda_url=https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh
wget -q ${__conda_url} -O miniconda.sh
  1. Installing miniconda through downloaded script. You can choose a different path for the install, here it is installed into the home directory.
__conda_path="~/miniconda3"
bash miniconda.sh -b -p ${__conda_path}
  1. Source conda to activate the installation for use.

source ${__conda_path}/etc/profile.d/conda.sh

Installing iGUIDE

The following commands should be called from within the iGUIDE directory (/path/to/iGUIDE/) after the repository is cloned. (If you need help on this part, just let me know).

  1. Install the conda environment from the requirements file. The name field here can be changed to what you would like to call the environment, default for the install script is 'iguide'.

conda env update --name=iguide --file etc/requirements.yml

  1. After successful creation of the environment, activate the iguide environment (or what you've called it).

conda activate iguide

  1. Install the supporting R-package into the environment.

R CMD INSTALL tools/iguideSupport

  1. Setup your environmental variables.
__iguide_dir=$(pwd)

echo -ne "#/bin/sh\nexport IGUIDE_DIR=${__iguide_dir}" > \
    ${CONDA_PREFIX}/etc/conda/activate.d/env_vars.sh

mkdir -p ${CONDA_PREFIX}/etc/conda/deactivate.d/

echo -ne "#/bin/sh\nunset IGUIDE_DIR" > \
    ${CONDA_PREFIX}/etc/conda/deactivate.d/env_vars.sh
  1. Install the command line interface for iGUIDE using pip.

pip install --upgrade tools/iguidelib/

  1. You should now deactivate and reactivate the environment to initiate the environmental variables.
conda deactivate
conda activate iguide

Testing

Tests to make sure the components were installed correctly.

  1. Test for required R-packages installed.

$(Rscript tools/rscripts/check_for_required_packages.R &> /dev/null) && echo true || echo false

  1. Check to make sure iguideSupport was installed correctly.

$(Rscript tools/rscripts/check_pkgs.R iguideSupport &> /dev/null) && echo true || echo false

  1. Run unit tests for iguideSupport.

`$(Rscript tools/rscripts/check_iguideSupport.R &> /dev/null) && echo true || echo false'

  1. Check to make sure the pip install of the CLI was successful.

command -v iguide &> /dev/null && echo true || echo false

  1. Run tests for iGUIDE, this step will take a little bit to complete if it starts processing the test case. Go grab a coffee, you deserve it getting to this point. :) The test will activate the environment as part of the test, so you should deactivate your environment first and then initiate the test.
conda deactivate
bash etc/tests/test.sh iguide
pmendez00 commented 4 years ago

Hi Chris,

Thanks for providing the manual installation. I've tried to install in two different OS:

In both OS, the installation of Miniconda3 is successful. However I'm having issues with the installation of iGUIDE with both OS during the 1st step (updating the environment of conda using /etc/requirements.yml.

In MacOS: gets stuck "Solving environment:" forever. Never finishes in both distributions of Ubuntu, the process of solving environment gets killed: "Solving environment: killed"

NOTE: I've tried to install iGUIDE in a freshly formated computer and with both Ubuntu versions, updated and upgraded, right before starting the installation.

I've checked if I was low in memory using the command $ free and there's plenty. however when checking the CPU and memory usage with command $ top after one point it takes over the 8 cores of the computer.

Do you have any suggestion on how to get the environment solved?

Thanks in advance.

Best,

Pedro. San Mateo, CA, 94403

Email: pmendez00@gmail.com Skype: pmendez00 Phone: +1 (650) 398-6653

LinkedIn: https://www.linkedin.com/in/pedro-mendez-linkedi/

This e-mail is privileged, confidential and contains private information. Any reading, retention, distribution or copy of this communication by any person other than its intended recipient is prohibited.

Este mensaje electrónico puede contener información confidencial o privilegiada. Si usted no es el destinatario del mensaje, o lo ha recibido por error, por favor notifíquelo al remitente y destruya el mensaje con todo su contenido. Está completamente prohibida cualquier copia, uso o distribución no autorizada del contenido de este mensaje.

On Mon, Jun 15, 2020 at 5:09 AM Chris Nobles notifications@github.com wrote:

Alright, let's try an manual install. I should likely update the docs with this process as well. If it's not clear, anything in the code blocks should be input into the command line. My preferred installation has both the miniconda and iGUIDE directories in my home directory. Installing miniconda

Skip to installing iGUIDE if you already have miniconda or anaconda installed. These can be executed in your home directory.

  1. Get the latest version of miniconda install script.

conda_url=https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh wget -q ${conda_url} -O miniconda.sh

  1. Installing miniconda through downloaded script. You can choose a different path for the install, here it is installed into the home directory.

__conda_path="~/miniconda3" bash miniconda.sh -b -p ${__conda_path}

  1. Source conda to activate the installation for use.

source ${__conda_path}/etc/profile.d/conda.sh Installing iGUIDE

The following commands should be called from within the iGUIDE directory (/path/to/iGUIDE/) after the repository is cloned. (If you need help on this part, just let me know).

  1. Install the conda environment from the requirements file. The name field here can be changed to what you would like to call the environment, default for the install script is 'iguide'.

conda env update --name=iguide --file etc/requirements.yml

  1. After successful creation of the environment, activate the iguide environment (or what you've called it).

conda activate iguide

  1. Install the supporting R-package into the environment.

R CMD INSTALL tools/iguideSupport

  1. Setup your environmental variables.

__iguide_dir=$(pwd)

echo -ne "#/bin/sh\nexport IGUIDE_DIR=${__iguide_dir}" > \ ${CONDA_PREFIX}/etc/conda/activate.d/env_vars.sh

mkdir -p ${CONDA_PREFIX}/etc/conda/deactivate.d/

echo -ne "#/bin/sh\nunset IGUIDE_DIR" > \ ${CONDA_PREFIX}/etc/conda/deactivate.d/env_vars.sh

  1. Install the command line interface for iGUIDE using pip.

pip install --upgrade tools/iguidelib/

  1. You should now deactivate and reactivate the environment to initiate the environmental variables.

conda deactivate conda activate iguide

Testing

Tests to make sure the components were installed correctly.

  1. Test for required R-packages installed.

$(Rscript tools/rscripts/check_for_required_packages.R &> /dev/null) && echo true || echo false

  1. Check to make sure iguideSupport was installed correctly.

$(Rscript tools/rscripts/check_pkgs.R iguideSupport &> /dev/null) && echo true || echo false

  1. Run unit tests for iguideSupport.

`$(Rscript tools/rscripts/check_iguideSupport.R &> /dev/null) && echo true || echo false'

  1. Check to make sure the pip install of the CLI was successful.

command -v iguide &> /dev/null && echo true || echo false

  1. Run tests for iGUIDE, this step will take a little bit to complete if it starts processing the test case. Go grab a coffee, you deserve it getting to this point. :) The test will activate the environment as part of the test, so you should deactivate your environment first and then initiate the test.

conda deactivate bash etc/tests/test.sh iguide

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cnobles commented 4 years ago

Really sorry about that, I made a mistake when I was writing the manual install earlier. I had you build the environment from the requirements file, but it's suppose to be built using the build file. This bypasses the environmental solving which can take some time. Try the updated install below and let me know how it goes. My preferred installation has both the miniconda and iGUIDE directories in my home directory.

Installing miniconda

Skip to installing iGUIDE if you already have miniconda or anaconda installed. These can be executed in your home directory.

  1. Get the latest version of miniconda install script.
__conda_url=https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh
wget -q ${__conda_url} -O miniconda.sh
  1. Installing miniconda through downloaded script. You can choose a different path for the install, here it is installed into the home directory.
__conda_path="~/miniconda3"
bash miniconda.sh -b -p ${__conda_path}
  1. Source conda to activate the installation for use.

source ${__conda_path}/etc/profile.d/conda.sh

Installing iGUIDE

The following commands should be called from within the iGUIDE directory (/path/to/iGUIDE/) after the repository is cloned. (If you need help on this part, just let me know).

  1. Install the conda environment from the requirements file. The name field here can be changed to what you would like to call the environment, default for the install script is 'iguide'. This is the part that changed from above.

conda create --name=iguide --quiet --yes --file etc/build.b1.0.1.txt

  1. After successful creation of the environment, activate the iguide environment (or what you've called it).

conda activate iguide

  1. Install the supporting R-package into the environment.

R CMD INSTALL tools/iguideSupport

  1. Setup your environmental variables.
__iguide_dir=$(pwd)

echo -ne "#/bin/sh\nexport IGUIDE_DIR=${__iguide_dir}" > \
    ${CONDA_PREFIX}/etc/conda/activate.d/env_vars.sh

mkdir -p ${CONDA_PREFIX}/etc/conda/deactivate.d/

echo -ne "#/bin/sh\nunset IGUIDE_DIR" > \
    ${CONDA_PREFIX}/etc/conda/deactivate.d/env_vars.sh
  1. Install the command line interface for iGUIDE using pip.

pip install --upgrade tools/iguidelib/

  1. You should now deactivate and reactivate the environment to initiate the environmental variables.
conda deactivate
conda activate iguide

Testing

Tests to make sure the components were installed correctly.

  1. Test for required R-packages installed.

$(Rscript tools/rscripts/check_for_required_packages.R &> /dev/null) && echo true || echo false

  1. Check to make sure iguideSupport was installed correctly.

$(Rscript tools/rscripts/check_pkgs.R iguideSupport &> /dev/null) && echo true || echo false

  1. Run unit tests for iguideSupport.

`$(Rscript tools/rscripts/check_iguideSupport.R &> /dev/null) && echo true || echo false'

  1. Check to make sure the pip install of the CLI was successful.

command -v iguide &> /dev/null && echo true || echo false

  1. Run tests for iGUIDE, this step will take a little bit to complete if it starts processing the test case. Go grab a coffee, you deserve it getting to this point. :) The test will activate the environment as part of the test, so you should deactivate your environment first and then initiate the test.
conda deactivate
bash etc/tests/test.sh iguide
pmendez00 commented 4 years ago

Hi Chris,

No worries at all. That happens to all of us. Thanks for your support. Now I can create the environment, install the R package, and setup the environment variables. However, when I try to Install the command line interface for iGUIDE using pip, I get the following error:

Any guidance? Thanks in advance!!

Cheers,

Pedro.

[image: image.png]

Pedro Mendez. San Mateo, CA, 94403 Email: pmendez00@gmail.com Skype: pmendez00 Phone: +1 (650) 398-6653

LinkedIn: https://www.linkedin.com/in/pedro-mendez-linkedi/

This e-mail is privileged, confidential and contains private information. Any reading, retention, distribution or copy of this communication by any person other than its intended recipient is prohibited.

Este mensaje electrónico puede contener información confidencial o privilegiada. Si usted no es el destinatario del mensaje, o lo ha recibido por error, por favor notifíquelo al remitente y destruya el mensaje con todo su contenido. Está completamente prohibida cualquier copia, uso o distribución no autorizada del contenido de este mensaje.

On Thu, Jun 18, 2020 at 5:27 AM Chris Nobles notifications@github.com wrote:

Really sorry about that, I made a mistake when I was writing the manual install earlier. I had you build the environment from the requirements file, but it's suppose to be built using the build file. This bypasses the environmental solving which can take some time. Try the updated install below and let me know how it goes. My preferred installation has both the miniconda and iGUIDE directories in my home directory. Installing miniconda

Skip to installing iGUIDE if you already have miniconda or anaconda installed. These can be executed in your home directory.

  1. Get the latest version of miniconda install script.

conda_url=https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh wget -q ${conda_url} -O miniconda.sh

  1. Installing miniconda through downloaded script. You can choose a different path for the install, here it is installed into the home directory.

__conda_path="~/miniconda3" bash miniconda.sh -b -p ${__conda_path}

  1. Source conda to activate the installation for use.

source ${__conda_path}/etc/profile.d/conda.sh Installing iGUIDE

The following commands should be called from within the iGUIDE directory (/path/to/iGUIDE/) after the repository is cloned. (If you need help on this part, just let me know).

  1. Install the conda environment from the requirements file. The name field here can be changed to what you would like to call the environment, default for the install script is 'iguide'. This is the part that changed from above.

conda create --name=iguide --quiet --yes --file etc/build.b1.0.1.txt

  1. After successful creation of the environment, activate the iguide environment (or what you've called it).

conda activate iguide

  1. Install the supporting R-package into the environment.

R CMD INSTALL tools/iguideSupport

  1. Setup your environmental variables.

__iguide_dir=$(pwd)

echo -ne "#/bin/sh\nexport IGUIDE_DIR=${__iguide_dir}" > \ ${CONDA_PREFIX}/etc/conda/activate.d/env_vars.sh

mkdir -p ${CONDA_PREFIX}/etc/conda/deactivate.d/

echo -ne "#/bin/sh\nunset IGUIDE_DIR" > \ ${CONDA_PREFIX}/etc/conda/deactivate.d/env_vars.sh

  1. Install the command line interface for iGUIDE using pip.

pip install --upgrade tools/iguidelib/

  1. You should now deactivate and reactivate the environment to initiate the environmental variables.

conda deactivate conda activate iguide

Testing

Tests to make sure the components were installed correctly.

  1. Test for required R-packages installed.

$(Rscript tools/rscripts/check_for_required_packages.R &> /dev/null) && echo true || echo false

  1. Check to make sure iguideSupport was installed correctly.

$(Rscript tools/rscripts/check_pkgs.R iguideSupport &> /dev/null) && echo true || echo false

  1. Run unit tests for iguideSupport.

`$(Rscript tools/rscripts/check_iguideSupport.R &> /dev/null) && echo true || echo false'

  1. Check to make sure the pip install of the CLI was successful.

command -v iguide &> /dev/null && echo true || echo false

  1. Run tests for iGUIDE, this step will take a little bit to complete if it starts processing the test case. Go grab a coffee, you deserve it getting to this point. :) The test will activate the environment as part of the test, so you should deactivate your environment first and then initiate the test.

conda deactivate bash etc/tests/test.sh iguide

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cnobles commented 4 years ago

Take 3. So the reason for the pip installation of the CLI failing was due to the environmental variables (IGUIDE_DIR) not being initiated. In step 4, we copy these environmental variables into the startup script for the environment. Since we wrote the data into the script, we haven't sourced the script to make the variables present in the environment. Switching steps 5 and 6 will resolve this issue. As least I has in my hands, as I was able to reproduce an error when following the above method at the pip installation. Remeber, my preferred installation has both the miniconda and iGUIDE directories in my home directory. If you have everything still set up, just activate the environment again and try the CLI pip installation. Otherwise, try the below method. If it works out for everyone, then I'll put this last method in the documentation as a manual installation process.

Installing miniconda

Skip to installing iGUIDE if you already have miniconda or anaconda installed. These can be executed in your home directory.

  1. Get the latest version of miniconda install script.
__conda_url=https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh
wget -q ${__conda_url} -O miniconda.sh
  1. Installing miniconda through downloaded script. You can choose a different path for the install, here it is installed into the home directory.
__conda_path="~/miniconda3"
bash miniconda.sh -b -p ${__conda_path}
  1. Source conda to activate the installation for use.

source ${__conda_path}/etc/profile.d/conda.sh

Installing iGUIDE

The following commands should be called from within the iGUIDE directory (/path/to/iGUIDE/) after the repository is cloned. (If you need help on this part, just let me know).

  1. Install the conda environment from the requirements file. The name field here can be changed to what you would like to call the environment, default for the install script is 'iguide'. This is the part that changed from above.

conda create --name=iguide --quiet --yes --file etc/build.b1.0.1.txt

  1. After successful creation of the environment, activate the iguide environment (or what you've called it).

conda activate iguide

  1. Install the supporting R-package into the environment.

R CMD INSTALL tools/iguideSupport

  1. Setup your environmental variables.
__iguide_dir=$(pwd)

echo -ne "#/bin/sh\nexport IGUIDE_DIR=${__iguide_dir}" > \
    ${CONDA_PREFIX}/etc/conda/activate.d/env_vars.sh

mkdir -p ${CONDA_PREFIX}/etc/conda/deactivate.d/

echo -ne "#/bin/sh\nunset IGUIDE_DIR" > \
    ${CONDA_PREFIX}/etc/conda/deactivate.d/env_vars.sh
  1. You should now deactivate and reactivate the environment to initiate the environmental variables.
conda deactivate
conda activate iguide
  1. Lastely, install the command line interface for iGUIDE using pip.

pip install --upgrade tools/iguidelib/

Testing

Tests to make sure the components were installed correctly.

  1. Test for required R-packages installed.

$(Rscript tools/rscripts/check_for_required_packages.R &> /dev/null) && echo true || echo false

  1. Check to make sure iguideSupport was installed correctly.

$(Rscript tools/rscripts/check_pkgs.R iguideSupport &> /dev/null) && echo true || echo false

  1. Run unit tests for iguideSupport.

`$(Rscript tools/rscripts/check_iguideSupport.R &> /dev/null) && echo true || echo false'

  1. Check to make sure the pip install of the CLI was successful.

command -v iguide &> /dev/null && echo true || echo false

  1. Run tests for iGUIDE, this step will take a little bit to complete if it starts processing the test case. Go grab a coffee, you deserve it getting to this point. :) The test will activate the environment as part of the test, so you should deactivate your environment first and then initiate the test.
conda deactivate
bash etc/tests/test.sh iguide
pmendez00 commented 4 years ago

Hi Chris,

It worked!! Thanks a lot.

I'll start running the sample dataset and hopefully we can soon start our experiments with Cas9 edited cells.

I'll keep you posted on the progress!

Again thanks for your help and for putting together iguide!

Cheers,

Pedro.

Pedro Mendez. San Mateo, CA, 94403 Email: pmendez00@gmail.com Skype: pmendez00 Phone: +1 (650) 398-6653

LinkedIn: https://www.linkedin.com/in/pedro-mendez-linkedi/

This e-mail is privileged, confidential and contains private information. Any reading, retention, distribution or copy of this communication by any person other than its intended recipient is prohibited.

Este mensaje electrónico puede contener información confidencial o privilegiada. Si usted no es el destinatario del mensaje, o lo ha recibido por error, por favor notifíquelo al remitente y destruya el mensaje con todo su contenido. Está completamente prohibida cualquier copia, uso o distribución no autorizada del contenido de este mensaje.

On Sat, Jun 20, 2020 at 8:52 AM Chris Nobles notifications@github.com wrote:

Take 3. So the reason for the pip installation of the CLI failing was due to the environmental variables (IGUIDE_DIR) not being initiated. In step 4, we copy these environmental variables into the startup script for the environment. Since we wrote the data into the script, we haven't sourced the script to make the variables present in the environment. Switching steps 5 and 6 will resolve this issue. As least I has in my hands, as I was able to reproduce an error when following the above method at the pip installation. Remeber, my preferred installation has both the miniconda and iGUIDE directories in my home directory. If you have everything still set up, just activate the environment again and try the CLI pip installation. Otherwise, try the below method. If it works out for everyone, then I'll put this last method in the documentation as a manual installation process. Installing miniconda

Skip to installing iGUIDE if you already have miniconda or anaconda installed. These can be executed in your home directory.

  1. Get the latest version of miniconda install script.

conda_url=https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh wget -q ${conda_url} -O miniconda.sh

  1. Installing miniconda through downloaded script. You can choose a different path for the install, here it is installed into the home directory.

__conda_path="~/miniconda3" bash miniconda.sh -b -p ${__conda_path}

  1. Source conda to activate the installation for use.

source ${__conda_path}/etc/profile.d/conda.sh Installing iGUIDE

The following commands should be called from within the iGUIDE directory (/path/to/iGUIDE/) after the repository is cloned. (If you need help on this part, just let me know).

  1. Install the conda environment from the requirements file. The name field here can be changed to what you would like to call the environment, default for the install script is 'iguide'. This is the part that changed from above.

conda create --name=iguide --quiet --yes --file etc/build.b1.0.1.txt

  1. After successful creation of the environment, activate the iguide environment (or what you've called it).

conda activate iguide

  1. Install the supporting R-package into the environment.

R CMD INSTALL tools/iguideSupport

  1. Setup your environmental variables.

__iguide_dir=$(pwd)

echo -ne "#/bin/sh\nexport IGUIDE_DIR=${__iguide_dir}" > \ ${CONDA_PREFIX}/etc/conda/activate.d/env_vars.sh

mkdir -p ${CONDA_PREFIX}/etc/conda/deactivate.d/

echo -ne "#/bin/sh\nunset IGUIDE_DIR" > \ ${CONDA_PREFIX}/etc/conda/deactivate.d/env_vars.sh

  1. You should now deactivate and reactivate the environment to initiate the environmental variables.

conda deactivate conda activate iguide

  1. Lastely, install the command line interface for iGUIDE using pip.

pip install --upgrade tools/iguidelib/ Testing

Tests to make sure the components were installed correctly.

  1. Test for required R-packages installed.

$(Rscript tools/rscripts/check_for_required_packages.R &> /dev/null) && echo true || echo false

  1. Check to make sure iguideSupport was installed correctly.

$(Rscript tools/rscripts/check_pkgs.R iguideSupport &> /dev/null) && echo true || echo false

  1. Run unit tests for iguideSupport.

`$(Rscript tools/rscripts/check_iguideSupport.R &> /dev/null) && echo true || echo false'

  1. Check to make sure the pip install of the CLI was successful.

command -v iguide &> /dev/null && echo true || echo false

  1. Run tests for iGUIDE, this step will take a little bit to complete if it starts processing the test case. Go grab a coffee, you deserve it getting to this point. :) The test will activate the environment as part of the test, so you should deactivate your environment first and then initiate the test.

conda deactivate bash etc/tests/test.sh iguide

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pmendez00 commented 4 years ago

Hi Chris,

Today, I wanted to get some files to play around with iGuide and I got stuck in the first step.

apparently is having issues exiting from iguide. Any guidance?

Thanks!

Pedro.

[image: image.png]

Pedro Mendez. San Mateo, CA, 94403 Email: pmendez00@gmail.com Skype: pmendez00 Phone: +1 (650) 398-6653

LinkedIn: https://www.linkedin.com/in/pedro-mendez-linkedi/

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On Fri, Jun 26, 2020 at 11:10 PM Pedro Mendez pmendez00@gmail.com wrote:

Hi Chris,

It worked!! Thanks a lot.

I'll start running the sample dataset and hopefully we can soon start our experiments with Cas9 edited cells.

I'll keep you posted on the progress!

Again thanks for your help and for putting together iguide!

Cheers,

Pedro.

Pedro Mendez. San Mateo, CA, 94403 Email: pmendez00@gmail.com Skype: pmendez00 Phone: +1 (650) 398-6653

LinkedIn: https://www.linkedin.com/in/pedro-mendez-linkedi/

This e-mail is privileged, confidential and contains private information. Any reading, retention, distribution or copy of this communication by any person other than its intended recipient is prohibited.

Este mensaje electrónico puede contener información confidencial o privilegiada. Si usted no es el destinatario del mensaje, o lo ha recibido por error, por favor notifíquelo al remitente y destruya el mensaje con todo su contenido. Está completamente prohibida cualquier copia, uso o distribución no autorizada del contenido de este mensaje.

On Sat, Jun 20, 2020 at 8:52 AM Chris Nobles notifications@github.com wrote:

Take 3. So the reason for the pip installation of the CLI failing was due to the environmental variables (IGUIDE_DIR) not being initiated. In step 4, we copy these environmental variables into the startup script for the environment. Since we wrote the data into the script, we haven't sourced the script to make the variables present in the environment. Switching steps 5 and 6 will resolve this issue. As least I has in my hands, as I was able to reproduce an error when following the above method at the pip installation. Remeber, my preferred installation has both the miniconda and iGUIDE directories in my home directory. If you have everything still set up, just activate the environment again and try the CLI pip installation. Otherwise, try the below method. If it works out for everyone, then I'll put this last method in the documentation as a manual installation process. Installing miniconda

Skip to installing iGUIDE if you already have miniconda or anaconda installed. These can be executed in your home directory.

  1. Get the latest version of miniconda install script.

conda_url=https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh wget -q ${conda_url} -O miniconda.sh

  1. Installing miniconda through downloaded script. You can choose a different path for the install, here it is installed into the home directory.

__conda_path="~/miniconda3" bash miniconda.sh -b -p ${__conda_path}

  1. Source conda to activate the installation for use.

source ${__conda_path}/etc/profile.d/conda.sh Installing iGUIDE

The following commands should be called from within the iGUIDE directory (/path/to/iGUIDE/) after the repository is cloned. (If you need help on this part, just let me know).

  1. Install the conda environment from the requirements file. The name field here can be changed to what you would like to call the environment, default for the install script is 'iguide'. This is the part that changed from above.

conda create --name=iguide --quiet --yes --file etc/build.b1.0.1.txt

  1. After successful creation of the environment, activate the iguide environment (or what you've called it).

conda activate iguide

  1. Install the supporting R-package into the environment.

R CMD INSTALL tools/iguideSupport

  1. Setup your environmental variables.

__iguide_dir=$(pwd)

echo -ne "#/bin/sh\nexport IGUIDE_DIR=${__iguide_dir}" > \ ${CONDA_PREFIX}/etc/conda/activate.d/env_vars.sh

mkdir -p ${CONDA_PREFIX}/etc/conda/deactivate.d/

echo -ne "#/bin/sh\nunset IGUIDE_DIR" > \ ${CONDA_PREFIX}/etc/conda/deactivate.d/env_vars.sh

  1. You should now deactivate and reactivate the environment to initiate the environmental variables.

conda deactivate conda activate iguide

  1. Lastely, install the command line interface for iGUIDE using pip.

pip install --upgrade tools/iguidelib/ Testing

Tests to make sure the components were installed correctly.

  1. Test for required R-packages installed.

$(Rscript tools/rscripts/check_for_required_packages.R &> /dev/null) && echo true || echo false

  1. Check to make sure iguideSupport was installed correctly.

$(Rscript tools/rscripts/check_pkgs.R iguideSupport &> /dev/null) && echo true || echo false

  1. Run unit tests for iguideSupport.

`$(Rscript tools/rscripts/check_iguideSupport.R &> /dev/null) && echo true || echo false'

  1. Check to make sure the pip install of the CLI was successful.

command -v iguide &> /dev/null && echo true || echo false

  1. Run tests for iGUIDE, this step will take a little bit to complete if it starts processing the test case. Go grab a coffee, you deserve it getting to this point. :) The test will activate the environment as part of the test, so you should deactivate your environment first and then initiate the test.

conda deactivate bash etc/tests/test.sh iguide

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