Dependency checking: The RMblast engine is not installed in RepeatMasker

[Prabhu89-code]

Dear OuShuJun, I am trying to use LTR_retriever. I have encountered the "Dependency checking: The RMblast engine is not installed in RepeatMasker" issue.

Yes, I followed the posts on same issue. Though I tried all I cannot solve it.

My question is how to INSTALL "RMBlast". May be my RMBlast installation could be wrong.

What I done was,

1. Downloaded the linux version of rmblast,
2. Extracted tar file into rmblast-2.11.0 it in /usr/local/ and another time in the repeatmasker folder.
3. After extraction do we need to give any comment for installation or simply invoke the path during RepeatMasker run/rerun process.

Kindly help me to solve this issue.

Thanking you!

[oushujun]

Hello, the easiest way is to install conda, then use conda to install LTR_retriever and dependencies.

Best, Shujun

On Fri, May 14, 2021 at 4:17 PM Prabhu89-code @.***> wrote:

Dear OuShuJun, I am trying to use LTR_retriever. I have encountered the "Dependency checking: The RMblast engine is not installed in RepeatMasker" issue.

Yes, I followed the posts on same issue. Though I tried all I cannot solve it.

My question is how to INSTALL "RMBlast". May be my RMBlast installation could be wrong.

What I done was,

1. Downloaded the linux version of rmblast,
2. Extracted tar file into rmblast-2.11.0 it in /usr/local/ and another time in the repeatmasker folder.
3. After extraction do we need to give any comment for installation or simply invoke the path during RepeatMasker run/rerun process.

Kindly help me to solve this issue.

Thanking you!

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[Prabhu89-code]

Yes, I tried both manual and conda for LTR_retreiver. Both have resulted with issue on "RMblast engine is not installed in RepeatMasker".

[oushujun]

Did you create an isolated env for conda? If you continuously encounter the repeatMasker issue, you may reinstall repeatMasker in the conda env and LTR_retriever should be able to pick it up automatically.

Shujun

On Fri, May 14, 2021 at 4:23 PM Prabhu89-code @.***> wrote:

Yes, I tried both manual and conda for LTR_retreiver. Both have resulted with issue on "RMblast engine is not installed in RepeatMasker".

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[Prabhu89-code]

Dear Dr. OuShuJun, Thank you for your reply.

     I don't really understand what is "isolated env for conda" ?

I done LTR conda version installation as follows:

conda create -n LTR_retriever source activate LTR_retriever git clone https://github.com/oushujun/LTR_retriever.git ./LTR_retriever/LTR_retriever -h

For installation of repeatmasker using CONDA always failed. So I downloaded "repeatmasker" extract it perl ./configure and give all the dependencies path.

In case of rmblast, I extracted it in /usr/local/RepeatMasker.

Could kindly correct me what I have done wrongly ?

Thank you very much !

Regards, Prabhu, S

[oushujun]

After source activate, did you do the installation with conda install -c bioconda ltr_retriever?

On Sat, May 15, 2021 at 2:08 PM Prabhu89-code @.***> wrote:

Dear Dr. OuShuJun, Thank you for your reply.

 I don't really understand what is "isolated env for conda" ?

I done LTR conda version installation as follows:

conda create -n LTR_retriever source activate LTR_retriever git clone https://github.com/oushujun/LTR_retriever.git ./LTR_retriever/LTR_retriever -h

For installation of repeatmasker using CONDA always failed. So I downloaded "repeatmasker" extract it perl ./configure and give all the dependencies path.

In case of rmblast, I extracted it in /usr/local/RepeatMasker.

Could kindly correct me what I have done wrongly ?

Thank you very much !

Regards, Prabhu, S

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[Prabhu89-code]

Yes I done conda install -c bioconda ltr_retriever.

It prepared another folder in the LTR_env as "LTR_retriever" and installed with database, bin, LTR_retreiver etc... folders

[Prabhu89-code]

Dear Dr.Ou Shu Jun, I successfully run the LTR_Retriever. I overcome the RMBlast dependency issue by following strategy posted from other comments in your github.

conda create -n EDTA python=3.6 conda activate EDTA conda install -y -c anaconda biopython pandas glob2 scikit-learn=0.19.0 conda config --add channels conda-forge conda config --add channels biocore conda config --add channels bioconda conda install -y -c cyclus java-jdk conda install -y repeatmodeler repeatmasker git clone https://github.com/oushujun/EDTA ./EDTA/EDTA.pl

I add path of EDTA bin (where all the dependencies are installed) to bash and run the LTR_Retriever. It is successfully running. Afterwards, I will do analysis of LTR results. If you are ok, can I send you mail regard analysis o LTR results ?

Thanking you!

Regards, Prabhu, S

[oushujun]

Hi Prabhu,

I am glad you found the way that works! I would like to keep discussions on github as much as possible so that other people can benefit from it just like you did from other discussions. I am closing this issue since it's resolved. Please open new issues for new questions.

Best, Shujun