Installing trans ABySS

[JManuelMonroyKuhn]

Hello!
I am trying to install trans ABySS in a cluster. I do not have root access and I have now almost everything installed to run the program except python igraph.

I tried installing python igraph like this
python setup.py install --user

But at the end I got this error

/usr/bin/ld: /usr/lib64/libxml2.a(entities.o): relocation R_X86_64_32 against `.text' can not be used when making a shared object; recompile with -fPIC
/usr/lib64/libxml2.a: could not read symbols: Bad value
collect2: error: ld returned 1 exit status
error: command 'gcc' failed with exit status 1

Anybody can advice me how to install it? Patience with me please! My knowledge of informatics is not great
Thanks

[GenoMax]

This one is going to be tougher to tackle (unless you can compile someplace else other than this cluster). Ask your admins about this (nicely ). This cluster uses SuSE correct?

https://lists.nongnu.org/archive/html/igraph-help/2014-05/msg00045.html

https://github.com/igraph/igraph/issues/640

https://lists.nongnu.org/archive/html/igraph-help/2014-05/msg00045.html

Wonder if compiling libxml2 in your own directory with -fPIC option would work.

[JManuelMonroyKuhn]

Hello!
I am not sure but probably it uses SuSe. It is the linux cluster of Leibniz Supercomputing Centre, so my guess will be it does.
Thanks I'll see what I can do

[JManuelMonroyKuhn]

Hello!
I compile libxml2 in my home directory and I added it to me PATH but it does not work. I got the same error and I dont know how to make it use libxml2 of my home directory.
I guess I will have to wait for an answer from the cluster administrators.

[GenoMax]

You could try to edit the Makefile and see if you can replace any pointers to system libxml2 (/usr/lib64/libxml2.a?) to your local one.

Have you emailed the developer of trans ABySS to see if an alternate libxml can be specified on the configure command line?