ete3 installation - conda not installing fasttree, clustalo, and probcons

[sarifkin]

I could use some help troubleshooting an installation problem.  I've attached a text file that has the output from my installation attempt. I installed using conda but ete3 build doesn't work because three helper applications don't seem to be installed.  I've tried both python 2.7 and python 3.4

Mac, OS 10.9.5.  

Thanks
Scott

[Jaime Huerta Cepas]

Hi Scott, 

it might be that some binaries were compiled in more recent OS and are not compatible with OSX 10.9.5.  

is there any error message if you try to execute any of those directly? For instance: 

/Users/HD/local/programs/anaconda/envs/phylo27/bin/ete3_apps/bin/clustalo

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[sarifkin]

Thanks Jaime,

Here is what I get when I run that (same error if I try fasttree - I also tried mafft which is fine in ete3 build and that worked here too). For probcons it is the same thing except instead of libgomp.1.dylib it is libstdc++.6.dylib


(phylo27)  $ /Users/HD/local/programs/anaconda/envs/phylo27/bin/ete3_apps/bin/clustalo
dyld: lazy symbol binding failed: Symbol not found: ___emutls_get_address
  Referenced from: /Users/HD/local/programs/anaconda/envs/phylo27/bin/ete3_apps/bin/../../../lib//./libgomp.1.dylib
  Expected in: /usr/local/lib/libgcc_s.1.dylib

dyld: Symbol not found: ___emutls_get_address
  Referenced from: /Users/HD/local/programs/anaconda/envs/phylo27/bin/ete3_apps/bin/../../../lib//./libgomp.1.dylib
  Expected in: /usr/local/lib/libgcc_s.1.dylib

Trace/BPT trap: 5



It seems that this __emutls_get_address problem shows up in other contexts (e.g. http://stackoverflow.com/questions/18938483/matplotlib-import-error-python)
 I tried the solution in that thread (with the appropriate directory) but it then gave me a different symbol not found error.

[sarifkin]

As a note - I tried installing it on another computer also running 10.9.5, and both the 'ete3 build check' and running the programs as you suggest above worked.  So it is something odd specifically about my computer's configuration.  Given that, it might be difficult to track down - thanks for any ideas!

[Renato Alves]

On your computer can you run:

unset LD_LIBRARY_PATH

on a terminal and try again on the same terminal?

On 31/01/17 19:13, sarifkin wrote:
>
> As a note - I tried installing it on another computer also running 10.9.5, and both the 'ete3 build check' and running the programs as you suggest above worked. So it is something odd specifically about my computer's configuration. Given that, it might be difficult to track down - thanks for any ideas!
>
>
>

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[Jaime Huerta Cepas]

in OSX you may actually need: 

unset DYLD_LIBRARY_PATH

On 31 January 2017 at 19:43, Renato Alves <alve...@gmail.com> wrote:

On your computer can you run:

unset LD_LIBRARY_PATH

on a terminal and try again on the same terminal?



On 31/01/17 19:13, sarifkin wrote:
>
> As a note - I tried installing it on another computer also running 10.9.5, and both the 'ete3 build check' and running the programs as you suggest above worked.  So it is something odd specifically about my computer's configuration.  Given that, it might be difficult to track down - thanks for any ideas!
>
>
>
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[sarifkin]

That did it!  I ran unset DYLD_LIBRARY_PATH. Thanks very much.  Now ete3 build check reports all of them OK and the standalone reports:

$ /Users/HD/local/programs/anaconda/envs/phylo27/bin/ete3_apps/bin/clustalo
FATAL: No sequence input was provided. For more information try: --help

which looks right since I didn't give it any sequences.


One additional question - what does this command do and will unsetting it mess me up in other programs?

[Renato Alves]

On 31/01/17 19:55, sarifkin wrote:
> That did it! I ran unset DYLD_LIBRARY_PATH. Thanks very much. Now ete3 build check reports all of them OK and the standalone reports:
>
> $ /Users/HD/local/programs/anaconda/envs/phylo27/bin/ete3_apps/bin/clustalo
> FATAL: No sequence input was provided. For more information try: --help

This command removes the variable DYLD_LIBRARY_PATH from the environment. It only affects that terminal

> which looks right since I didn't give it any sequences.
>
>
> One additional question - what does this command do and will unsetting it mess me up in other programs?

Yes, other programs may be affected but only if you launch them from that terminal session.
So programs make use of this special variable to include additional libraries without affecting the system.
While this is fine for individual programs, it has undesired effects if set globally.
Sadly setting it globally (via ~/.bashrc, ~/.profile or some other way) is often recommended.

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