problem in trinity installation
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4.5 years ago
majeedaasim ▴ 60

I am using ubunto 16.4 I tried to install trinity by following the instructions on the web. After downloading and extracting, I typed "make" the "make plugins" Then I ran trinity on test data as mentioned i.e byu typing "./runMe.sh" but following error is shown:

Error, cannot locate Trinity-specific tool: ParaFly in the PATH setting: /home/aasim/Aasim/bin/Trinity-v2.5.1/trinity-plugins/BIN:/home/aasim/anaconda3/bin:/home/aasim/Aasim/bin/RubyCAOS/RubyCAOS/bin:/home/aasim/bin:/home/aasim/.local/bin:/home/aasim/anaconda3/bin:/home/aasim/anaconda3/bin:/home/aasim/bin:/home/aasim/.local/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin:/usr/lib/jvm/java-8-oracle/bin:/usr/lib/jvm/java-8-oracle/db/bin:/usr/lib/jvm/java-8-oracle/jre/bin,  be sure to install Trinity by running 'make' in the base installation directory
TRinity installation error • 3.5k views
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Did you get errors when you initially did make in the main Trinity directory?

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yes I got an error .

Using gnu compiler for Inchworm and Chrysalis
cd Inchworm && make
make[1]: Entering directory '/home/aliviya21/BIONIVID/trinityrnaseq-v2.13.0/Inchworm'
mkdir -p build
cd build && cmake -DCMAKE_INSTALL_PREFIX="" ../ && make DESTDIR=../ install
/bin/sh: 1: cmake: not found
Makefile:2: recipe for target 'all' failed
make[1]: *** [all] Error 127
make[1]: Leaving directory '/home/aliviya21/BIONIVID/trinityrnaseq-v2.13.0/Inchworm'
Makefile:31: recipe for target 'inchworm_target' failed
make: *** [inchworm_target] Error 2

. this is the error report

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It would be best to use conda to install the program.

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I tried but still getting errors.

Collecting package metadata (current_repodata.json): done Solving environment: failed with initial frozen solve. Retrying with flexible solve. Collecting package metadata (repodata.json): done Solving environment: failed with initial frozen solve. Retrying with flexible solve.

PackagesNotFoundError: The following packages are not available from current channels:

  • trinityrnaseq-v2.13.0

Current channels:

To search for alternate channels that may provide the conda package you're looking for, navigate to

https://anaconda.org

and use the search bar at the top of the page.

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I see you have anaconda on your PATH, can't you install Trinity with conda install trinity?

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