PDB2PQR (http://sourceforge.net/projects/pdb2pqr) 1.4.0 was released on 2009/4/3. Please add it to the Portage tree.
Added first version to sci overlay: 1. Should be the bumped version of 1.3.0 2. numeric automagics removed 3. installation via make 4. opal support not yet included 5. pydoc and examples installation is now optional 6. LDFLAGS will be respected
(In reply to comment #1) > 4. opal support not yet included Is there an issue with the Opal implementation, or is there just not support in the ebuild for the --with-opal flag? Also, what about --with-apbs & --with-apbs-opal, and the web interface? Thanks!
It is just not included for some reasons: 1. I want to get the basic functions to run --> done 2. I am not really sure how to setup the opal thing correctly 3. I don't know how I should correctly include the webserver support :) Today I love lists. I will take a look in it the next days. First I have to fix the apbs ebuild, means remove opal and double things there. Its not included but it will come asap.
(In reply to comment #3) > 1. I want to get the basic functions to run --> done What problems are you having exactly? I might be able to help you out. > 2. I am not really sure how to setup the opal thing correctly Please take a look at http://baja.wustl.edu/~srunni/files/pdb2pqr-1.4.0-documentation.pdf (mirrored at http://omploader.org/vMWticA/pdb2pqr-1.4.0-documentation.pdf) for information on configuring/installing PDB2PQR 1.4.0 with Opal support. > 3. I don't know how I should correctly include the webserver support The PDF linked above also covers how to configure/install the PDB2PQR/APBS web interface. > I will take a look in it the next days. First I have to fix the apbs ebuild, > means remove opal and double things there. A PDB2PQR --> APBS --> $visualization_software pipeline is now included in PDB2PQR (also covered in the PDF; the visualization step is experimental), so you might want to check both ebuilds to make sure they're working in conjuction before adding either one to the Portage tree.
(In reply to comment #4) > (In reply to comment #3) > > 1. I want to get the basic functions to run --> done > > What problems are you having exactly? I might be able to help you out. Bad build system, not respecting FLAGS, installing src code etc. But that is fixed. > > > 2. I am not really sure how to setup the opal thing correctly > > Please take a look at > http://baja.wustl.edu/~srunni/files/pdb2pqr-1.4.0-documentation.pdf (mirrored > at http://omploader.org/vMWticA/pdb2pqr-1.4.0-documentation.pdf) for > information on configuring/installing PDB2PQR 1.4.0 with Opal support. Doesn't help > > > 3. I don't know how I should correctly include the webserver support > > The PDF linked above also covers how to configure/install the PDB2PQR/APBS web > interface. > See above. > > I will take a look in it the next days. First I have to fix the apbs ebuild, > > means remove opal and double things there. > > A PDB2PQR --> APBS --> $visualization_software pipeline is now included in > PDB2PQR (also covered in the PDF; the visualization step is experimental), so > you might want to check both ebuilds to make sure they're working in conjuction > before adding either one to the Portage tree. > Thanks for that advice.
(In reply to comment #5) > Doesn't help Can you post some of the errors you're getting?
(In reply to comment #6) > (In reply to comment #5) > > Doesn't help > > Can you post some of the errors you're getting? > That doesn't help inside an ebuild. Which URL should be set, as this is a quite personal setting. And it install the webstuff into the PDB2PQR dir and not in a webroot as it should do. You can read about the web-app eclass and propose a clean way to switch between client-only and server, as well as a gentoo way of installing a vhost.
(In reply to comment #7) > Which URL should be set, as this is a quite personal setting. Well, the user decides when running the calculation command. If a URL isn't specified, it defaults to the NBCR's Opal grid (http://nbcr.net/services/opal). > And it install the webstuff into the PDB2PQR dir and not in a webroot as it should do. That is true, but is also something that can't be easily fixed. What I do right now is install PDB2PQR itself into the webroot (i.e., --prefix=/var/www/pdb2pqr). There isn't really a better solution. > You can read about the web-app eclass and propose a clean way to switch > between client-only and server As of right now, there is no clean way. None of the examples for webapp.eclass cover how to install an application that has both command-line and web interfaces. If there is a precedent for handling such a situation, it should be followed. However, if there isn't a precedent, perhaps you could just copy the web interface-relevant files to the webroot during the install? > as well as a gentoo way of installing a vhost. Why is this difficult to do? I don't know much about this, but IIRC, you would just have the web interface files in /var/www/localhost/htdocs/pdb2pqr (or similar) and reference it from /var/db/webapps/pdb2pqr/1.4.0/installs.
(In reply to comment #8) > (In reply to comment #7) > > Which URL should be set, as this is a quite personal setting. > > Well, the user decides when running the calculation command. If a URL isn't > specified, it defaults to the NBCR's Opal grid (http://nbcr.net/services/opal). Isn't there anything which is alter by setting an URL at compiletime? > > > And it install the webstuff into the PDB2PQR dir and not in a webroot as it should do. > > That is true, but is also something that can't be easily fixed. What I do right > now is install PDB2PQR itself into the webroot (i.e., > --prefix=/var/www/pdb2pqr). There isn't really a better solution. Thats a NONO solution. > > > You can read about the web-app eclass and propose a clean way to switch > > between client-only and server > > As of right now, there is no clean way. None of the examples for webapp.eclass > cover how to install an application that has both command-line and web > interfaces. Check the jmol ebuild > > If there is a precedent for handling such a situation, it should be followed. > However, if there isn't a precedent, perhaps you could just copy the web > interface-relevant files to the webroot during the install? Something like that. > > > as well as a gentoo way of installing a vhost. > > Why is this difficult to do? I don't know much about this, but IIRC, you would > just have the web interface files in /var/www/localhost/htdocs/pdb2pqr (or > similar) and reference it from /var/db/webapps/pdb2pqr/1.4.0/installs. > Yes but the few lines have to be writing in an QA clean way. Go ahead and propose a solution. If you have questions or want to discuss join #gentoo-science at irc.freenode.net and ping me.
(In reply to comment #9) > Isn't there anything which is alter by setting an URL at compiletime? Yes, you have to set the URL for the web interface. That is done via the flag --with-url=<url>. If you don't set that flag, the web interface is not configured/installed. > Yes but the few lines have to be writing in an QA clean way. > > Go ahead and propose a solution. Is there some formal process for this? Where can I get a copy of the preliminary ebuild?
http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=tree or layman -a sci Just write your ideas and post them here or mail them to me. Any contributions to sci is always welcome. Are you subsrcibed to gentoo-science@lists.gentoo.org?
Mark this bug as fixed since 1.4.0 is in portage. Thanks, Markus
