Maybe this was a much simpler issue. In the first instance, after you added
the lines to your .bashrc, you need to source the .bashrc file by typing
"source .bashrc" in the terminal. Otherwise the changes you made to .bashrc
will not be affected. From your initial message, I am assuming you did not
source .bashrc or amber.sh and hence the modules might not have been loaded.
In the second instance, you sourced the Amber.sh file and that added the
required path variables to your current session even though you might not
have made changes to .bashrc.
Make the changes to your .bashrc and source it if you want the modules to
be automatically loaded for every session. Hope this clarifies the issue.
Best,
Koushik
On Tuesday, June 14, 2016, Hai Nguyen <nhai.qn.gmail.com> wrote:
> great.
>
> But I believe the mistake was from something else. Extra '/' does not
> really matter.
>
> Hai
>
> On Tue, Jun 14, 2016 at 11:21 PM, Abdul-Rashid Iii Sampaco <
> absampaco.up.edu.ph <javascript:;>> wrote:
>
> > Hi,
> >
> > It finally works! Thank you so much. My mistake was copying "source
> > /home/absampaco/amber16//amber.sh" directly to the terminal. It has one
> > extra '/'.
> >
> > On Wed, Jun 15, 2016 at 10:59 AM, Hai Nguyen <nhai.qn.gmail.com
> <javascript:;>> wrote:
> >
> > > hi
> > >
> > > it's clearly that you successfully installed all Python packages in
> > > $AMBERHOME/lib/python2.7/site-packages
> > >
> > > What did you mean about
> > >
> > > > It says it cannot find the file.
> > >
> > > *What is "it"?*
> > >
> > > Have you* source $AMBERHOME/amber.sh* (if you are using Bourne shell
> > (sh))
> > > or *source $AMBERHOME/amber.csh* (if you are using C shell) yet?
> > >
> > > Can you send your screen capture showing the failure?
> > >
> > > Hai
> > >
> > > On Tue, Jun 14, 2016 at 10:54 PM, Abdul-Rashid Iii Sampaco <
> > > absampaco.up.edu.ph <javascript:;>> wrote:
> > >
> > > > Here. I also included python2.7/site-packages/
> > > >
> > > > On Wed, Jun 15, 2016 at 10:48 AM, Hai Nguyen <nhai.qn.gmail.com
> <javascript:;>>
> > wrote:
> > > >
> > > > > Please see my reply below.
> > > > >
> > > > > On Tue, Jun 14, 2016 at 10:06 PM, Abdul-Rashid Iii Sampaco <
> > > > > absampaco.up.edu.ph <javascript:;>> wrote:
> > > > >
> > > > > > Thank you for all your responses.
> > > > > >
> > > > > > I tried Case's suggestion. I understand the command forces the
> > > computer
> > > > > to
> > > > > > download Miniconda. However, it fails to connect. The error
> message
> > > is:
> > > > > >
> > > > > > Connecting to repo.continuum.io (repo.continuum.io
> > > > > )|54.225.73.227|:443...
> > > > > > failed: Connection timed out
> > > > > >
> > > > > > I'm not sure if this is already a problem on my internet
> > connection,
> > > or
> > > > > how
> > > > > > my terminal connects to the internet. I opened the link manually
> on
> > > the
> > > > > > browser and downloaded the shell file. I then used ./configure
> > > > > > --with-python /path/to/miniconda.sh but it cannot be run by the
> > > > > terminal. I
> > > > > > understand now that the shell file cannot be run on the terminal.
> > Any
> > > > > > suggestions on how to run it?
> > > > > >
> > > > > > Btw, I also tried Nguyen's suggestion, but it does not work. It
> > says
> > > it
> > > > > > cannot find the file.
> > > > > >
> > > > > >
> > > > > Can you send the output of this
> > > > >
> > > > > *ls $AMBERHOME/lib/*
> > > > >
> > > > >
> > > > > > To Chagas, I don't know exactly what you mean by "Try to copy
> your
> > > > > content
> > > > > > and put it in the .profile file". Which content? I'm not an
> > > experienced
> > > > > > Linux user. I'm sorry if you have to be very specific on your
> > > > > instructions
> > > > > > to me.
> > > > > >
> > > > > > Sincerely,
> > > > > >
> > > > > > Rashid
> > > > > >
> > > > > > On Tue, Jun 14, 2016 at 10:25 PM, Hai Nguyen <nhai.qn.gmail.com
> <javascript:;>>
> > > > wrote:
> > > > > >
> > > > > > > Hi
> > > > > > >
> > > > > > > First, do you see any folder in
> > > > > $AMBERHOME/lib/python*X.Y*/site-packages?
> > > > > > > where "X.Y" can be *2.7, 3.4, 3.5* (you should expect to see
> > > parmed,
> > > > > > > sander, pytraj, ...)
> > > > > > >
> > > > > > > If yes, do this again in your terminal
> > > > > > >
> > > > > > > source /home/absampaco/amber16//amber.sh
> > > > > > >
> > > > > > > If nothing works, please try Case's suggestion.
> > > > > > >
> > > > > > > Hai
> > > > > > >
> > > > > > > On Tue, Jun 14, 2016 at 4:22 AM, Abdul-Rashid Iii Sampaco <
> > > > > > > absampaco.up.edu.ph <javascript:;>> wrote:
> > > > > > >
> > > > > > > > Hi,
> > > > > > > >
> > > > > > > > I am installing AmberTools16 on my laptop using Ubuntu
> BioLinux
> > > on
> > > > > VM.
> > > > > > I
> > > > > > > > followed all instructions on the guide. Based on what I see,
> > > > > everything
> > > > > > > > works perfectly well after make install. However, the 'make
> > test'
> > > > > gives
> > > > > > > > this error message:
> > > > > > > >
> > > > > > > > Error: Could not import Amber Python modules! Probably your
> > Amber
> > > > > > Python
> > > > > > > > environment was not set up correctly.
> > > > > > > >
> > > > > > > > I already added the test -f /home/absampaco/amber16//amber.sh
> > &&
> > > > > source
> > > > > > > > /home/absampaco/amber16//amber.sh to my ~/.bash.rc before the
> > > 'make
> > > > > > > > install'.
> > > > > > > >
> > > > > > > > I would appreciate any help given.
> > > > > > > > _______________________________________________
> > > > > > > > AMBER mailing list
> > > > > > > > AMBER.ambermd.org <javascript:;>
> > > > > > > > http://lists.ambermd.org/mailman/listinfo/amber
> > > > > > > >
> > > > > > > _______________________________________________
> > > > > > > AMBER mailing list
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> > > > > > > http://lists.ambermd.org/mailman/listinfo/amber
> > > > > > >
> > > > > > _______________________________________________
> > > > > > AMBER mailing list
> > > > > > AMBER.ambermd.org <javascript:;>
> > > > > > http://lists.ambermd.org/mailman/listinfo/amber
> > > > > >
> > > > > _______________________________________________
> > > > > AMBER mailing list
> > > > > AMBER.ambermd.org <javascript:;>
> > > > > http://lists.ambermd.org/mailman/listinfo/amber
> > > > >
> > > >
> > > > _______________________________________________
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> > > > http://lists.ambermd.org/mailman/listinfo/amber
> > > >
> > > >
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> > >
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Received on Tue Jun 14 2016 - 21:00:02 PDT
