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rivas-lab / nanopore

Tools for analysis of long-read sequencing data.
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nanopolish #16

Closed yk-tanigawa closed 7 years ago

yk-tanigawa commented 7 years ago

To run nanopolish, you need to have c++ dynamic libraries, which you can activate by loading gcc module on sherlock cluster.

[ytanigaw@sherlock-ln01 login_node ~/nanopolish]$ ml purge
[ytanigaw@sherlock-ln01 login_node ~/nanopolish]$ ./nanopolish_test 
./nanopolish_test: /usr/lib64/libstdc++.so.6: version `CXXABI_1.3.7' not found (required by ./nanopolish_test)
./nanopolish_test: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.20' not found (required by ./nanopolish_test)
./nanopolish_test: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.14' not found (required by ./nanopolish_test)
./nanopolish_test: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.21' not found (required by ./nanopolish_test)
[ytanigaw@sherlock-ln01 login_node ~/nanopolish]$ ml load gcc
[ytanigaw@sherlock-ln01 login_node ~/nanopolish]$ ./nanopolish_test 
===============================================================================
All tests passed (427 assertions in 5 test cases)
yk-tanigawa commented 7 years ago

It is now installed on sherlock

[ytanigaw@sherlock-ln01 login_node ~]$ which nanopolish
/share/PI/mrivas/bin/nanopolish