search

flass / pantagruel

a pipeline for reconciliation of phylogenetic histories within a bacterial pangenome
GNU General Public License v3.0
46 stars 7 forks source link

Java version and InterProScan #3

Closed ElitaJaun closed 5 years ago

ElitaJaun commented 5 years ago

Hi Florent,

Seem that Java version needs updating to run with InterProScan. Would you please be able to help out with this?

I get the following message:

pantagruel_pipeline/pantagruel/install_dependencies.sh: line 248: [: too many arguments Java version 1.8 is required to run InterProScan. Detected version 10.0 Please install the correct version. ERROR: Interproscan test was not successful

flass commented 5 years ago

OK this is due to a small bug introduced in previous commit 3be7cea to fix installation of Interproscan. This should be fixed with commit 5021d45. Please let me know.

ElitaJaun commented 5 years ago

Thank you - the java error has disappeared, I thought id better install it all again and Java error disappeared, but I now getting the following:

pantagruel_pipeline/pantagruel/install_dependencies.sh: line 212: interproscan: command not found get Interproscan 5.33-72.0 found InterProScan executable: /home/elita/pantagruel_pipeline/interproscan-5.33-72.0/interproscan.sh 22/02/2019 14:54:01:936 Welcome to InterProScan-5.33-72.0 usage: java -XX:+UseParallelGC -XX:ParallelGCThreads=2 -XX:+AggressiveOpts -XX:+UseFastAccessorMethods -Xms128M -Xmx2048M -jar interproscan-5.jar

then all option for analyses and it ends with this ERROR: Interproscan test was not successful

Do I need to do anything about this?

flass commented 5 years ago

this was a bug in the installation script. This is fixed with commit 99deaa4.