[phenixbb] phenix.phaser PATH problem

G P gysubscribe at gmail.com
Thu Jul 21 02:55:18 PDT 2011


Thanks, Francois!

To define a permanent variable and source it in bashrc. That's really a good
idea.
But Ralf's suggestion seems more amazing, why and how does the order of
source command in .bashrc affect? I am wondering.


On Thu, Jul 21, 2011 at 11:29 AM, Francois Berenger <berenger at riken.jp>wrote:

> I have this in my .bashrc, I use the command phenix_setup
> only before I start using phenix:
>
> ---
> # to use locally installed phenix
> function phenix_setup() {
>    PHENIX_ENV=\
> /usr/local/phenix-dev/phenix-**dev-756/phenix-dev-756/phenix_**env.sh
>    if [ -f $PHENIX_ENV ]; then
>        source $PHENIX_ENV
>    fi
> }
> ---
>
> I use the same kind of trick for CCP4.
>
> PS: You need to adapt this code to where your
>    phenix_env.sh is installed.
>
>
> On 07/21/2011 06:20 PM, G P wrote:
>
>> Hi Ralf,
>>
>> Thanks a lot for your help. I changed the order and it works now. But I
>> am wondering why? Is that means the .bashrc script will read lines from
>> down to up which allow it to see the line of source for phenix first?
>>
>> Thanks a lot again!
>>
>> cheers,
>> GP
>>
>> On Wed, Jul 20, 2011 at 10:35 PM, Ralf Grosse-Kunstleve
>> <rwgrosse-kunstleve at lbl.gov <mailto:rwgrosse-kunstleve@**lbl.gov<rwgrosse-kunstleve at lbl.gov>>>
>> wrote:
>>
>>    Hopefully, all you need to do is source phenix_env last.
>>    E.g. look in your .cshrc or .bashrc file with the phenix and ccp4
>>    source commands.
>>    Reorder the commands so that phenix comes after the ccp4 command.
>>    Then open a new shell and run "phenix.phaser params.eff" again.
>>    Could you try that?
>>    (I recommend against copying files from the phenix to the ccp4 tree.)
>>    Ralf
>>
>>    On Wed, Jul 20, 2011 at 11:21 AM, G P <gysubscribe at gmail.com
>>    <mailto:gysubscribe at gmail.com>**> wrote:
>>
>>        Dear all,
>>
>>        It's long story:
>>
>>        At beginning, I have phenix installed. I do not have CCP4
>>        installed. Then I run "phenix.phaser params.eff" to call phenix
>>        run phaser from script params.eff. It works well.
>>        Then, I installed CCP4 with its own phaser inside. Then I run
>>        again "phenix.phaser params.eff". The computer start to import
>>        files (should be some libraries and supporting files, not input
>>        data) from CCP4 installation directory. It seems so strange for me.
>>
>>        And because some of the .so files in CCP4 directory are for
>>        32bit, phenix.phaser gave me error message: wrong ELF class:
>>        ELFCLASS32 and refused to keep running. I guess I could solve
>>        this problem by copying the same .so file in phenix directory
>>        into CCP4's directory.
>>
>>        What I really want to know is why this happen. Is that the
>>        installation of CCP4 changed some kinds of PATH variables for
>>        phenix? How could I fix by giving a right path again?
>>
>>        I would appreciate to any help. Thanks a lot guys!
>>
>>        Best regards,
>>        GP
>>
>>
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>>
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