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cerebis / meta-sweeper

Parametric sweep of simulated microbial communities and metagenomic sequencing.
GNU General Public License v3.0
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bash_configure not setting environment variables #57

Closed koadman closed 7 years ago

koadman commented 7 years ago

It looks like the configuration script isn't doing it's job on my ubuntu 16.04 machine:

koadman@oneida:~/git/meta-sweeper$ echo $NXF_CLASSPATH

koadman@oneida:~/git/meta-sweeper$ ./bash_configure 
Setting up meta-sweeper environment variables
Checking for nextflow: [OK]
Checking for BEAGLE_LIB: Warning: BEAGLE_LIB not set. At runtime BEAST needs to locate libhmsbeagle-jni.so
Inferring meta-sweeper installation directory to be: /home/koadman/git/meta-sweeper
Extending Nextflow class path: NXF_CLASSPATH += /home/koadman/git/meta-sweeper
koadman@oneida:~/git/meta-sweeper$ echo $NXF_CLASSPATH

koadman@oneida:~/git/meta-sweeper$

it's not obvious to me why this is failing.

cerebis commented 7 years ago

It doesn't look like you set BEAGLE_LIB prior to sourcing bash_configure.

It should point to the directory containing the .so library.

Eg.

export BEAGLE_LIB=/usr/lib64

The script doesn't try to find the library itself. I can make it look in standard places, but for now this is left as the responsibility of the user.

On Tue, Nov 15, 2016 at 2:47 AM, Aaron Darling notifications@github.com wrote:

It looks like the configuration script isn't doing it's job on my ubuntu 16.04 machine:

koadman@oneida:~/git/meta-sweeper$ echo $NXF_CLASSPATH

koadman@oneida:~/git/meta-sweeper$ ./bash_configure Setting up meta-sweeper environment variables Checking for nextflow: [OK] Checking for BEAGLE_LIB: Warning: BEAGLE_LIB not set. At runtime BEAST needs to locate libhmsbeagle-jni.so Inferring meta-sweeper installation directory to be: /home/koadman/git/meta-sweeper Extending Nextflow class path: NXF_CLASSPATH += /home/koadman/git/meta-sweeper koadman@oneida:~/git/meta-sweeper$ echo $NXF_CLASSPATH

koadman@oneida:~/git/meta-sweeper$

it's not obvious to me why this is failing.

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cerebis commented 7 years ago

Also, per the documentation, this is a script that must be sourced rather than executed. Executed scripts will not export changed environmental variables to the current user shell.

koadman commented 7 years ago

yup, i missed the detail of sourcing vs. executing. looks good.