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Project Wiki Asterias wiki pages |
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DownloadPageMain.DownloadPage HistoryHide minor edits - Show changes to output May 16, 2007, at 01:24 PM
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* [[Python 2.4 -> http://www.python.org]] (and a bunch of Python 2.4 packages; fixme: be explicit). to:
* [[Python 2.4 -> http://www.python.org]] (and a bunch of standard Python 2.4 packages). Changed lines 165-166 from:
* [[R -> http://cran.r-project.org]] (2.2.0 or higher), and several R and BioC packages (fixme: be explicit). to:
* [[R -> http://cran.r-project.org]] (2.2.0 or higher), and several R and BioC packages. You might want to take a look at the scripts [[download.all.sh -> http://bioinformatics.org/asterias/bzr/adacgh/R-packages/download.all.packs.sh]] and [[install.all.packs.sh -> http://bioinformatics.org/asterias/bzr/adacgh/R-packages/install.all.packs.sh]], and modify them for your setting. They can help automate downloading and isntalling most of the dependencies. Added lines 186-202:
>>center<< !! Installation (web-based applications) >><< * Make sure you have installed and downloaded the above programs * You need the corresponding R code. For example, for genesrf, install the varSelRF R package, etc. * Configure your web server, so that requests for you installation are sent to right place. * Get MPI running. For all the applications that use MPI, the universes are started and stopped independently for each. [[Asterias common -> http://bioinformatics.org/asterias/bzr/Asterias-common/]] has several files that can be used as examples. Most of the applications call "tryRrun.py" and it is likely that you will need to modify the paths. Likewise, the files in Asterias-common provide examples for monitoring applications, logging, etc. Paths here will probably need to be modified. You will also probably need to change the IPs of the hosts of your cluster. * LAM/MPI is run by the web server user. We had to change the default shell for our apache user, so it could boot lam universes. ---- May 04, 2007, at 11:12 AM
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The code for the project is also mirrored at [[Launchpad -> http://launchpad.net/projects/asterias]]. You can check there for alternative ways to download (and somewhat more verbose comments with maybe more detail). to:
The code for the project is also mirrored at [[Launchpad -> http://launchpad.net/asterias]]. You can check there for alternative ways to download (and somewhat more verbose comments with maybe more detail). May 04, 2007, at 11:11 AM
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All the code for [[ADaCGH -> http://adacgh.bioinfo.cnio.es]]. This includes the stand-alone ADaCGH R package. The best is for you to grab the complete sources: to:
All the code for [[ADaCGH -> http://adacgh2.bioinfo.cnio.es]]. This includes the stand-alone ADaCGH R package. The best is for you to grab the complete sources: January 04, 2007, at 10:57 AM
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!! IDconverter and IDClight You know what do do already :-). Please note that we use databases which are not included in the download (they are huge, and they are periodically updated). @@bzr get http://bioinformatics.org/asterias/bzr/idconverter@@ @@bzr get http://bioinformatics.org/asterias/bzr/idclight@@ ----- January 03, 2007, at 01:02 PM
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This is a pre-alpha version of an attempt to make Asterias as easy to install as doing "easy_install asterias" (well, almost). But this is still pre-alpha (i.e., it does not really work). There are issues to solve both in the application code itself, and also figuring out a good way of having the paster server, asterias, and apache to get along well. You can get the code doing: to:
This is a pre-alpha version of an attempt to make Asterias as easy to install as doing "easy_install asterias" (well, almost). to clean up the code, to get rid of lots of code duplication, and to make the logic of the programs simpler. But this is still pre-alpha (i.e., it does not really work). There are issues to solve both in the application code itself, and also figuring out a good way of having the paster server, asterias, and apache to get along well. You can get the code doing: January 03, 2007, at 12:59 PM
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The code for the project is also mirrored at [[Launchpad -> http://launchpad.net/projects/asterias]]. You can check there for alternative ways to download. to:
The code for the project is also mirrored at [[Launchpad -> http://launchpad.net/projects/asterias]]. You can check there for alternative ways to download (and somewhat more verbose comments with maybe more detail). January 03, 2007, at 12:59 PM
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!! DNMAD All the code for [[DNMAD -> http://dnmad.bioinfo.cnio.es]]. Download it doing @@bzr get http://bioinformatics.org/asterias/bzr/dnmad@@ This differs from the rest of applications both in the language (Perl instead of Python) and some of the internal logic. ----- January 03, 2007, at 12:57 PM
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!! Asterias-pylons This is a pre-alpha version of an attempt to make Asterias as easy to install as doing "easy_install asterias" (well, almost). But this is still pre-alpha (i.e., it does not really work). There are issues to solve both in the application code itself, and also figuring out a good way of having the paster server, asterias, and apache to get along well. You can get the code doing: @@bzr get http://bioinformatics.org/asterias/bzr/asterias-pylons@@ ----- January 03, 2007, at 12:40 PM
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The code for the project is also mirrored at [[Launchpad -> http://launchpad.net/projects/asterias]]. to:
The code for the project is also mirrored at [[Launchpad -> http://launchpad.net/projects/asterias]]. You can check there for alternative ways to download. Deleted line 63:
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!! Tnasas All the code for [[Tnasas -> http://tnasas.bioinfo.cnio.es]]. Download it doing @@bzr get http://bioinformatics.org/asterias/bzr/tnasas@@ ----- December 29, 2006, at 09:41 AM
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!! SignS All the code for [[SignS -> http://signs.bioinfo.cnio.es]]. Download it doing @@bzr get http://bioinformatics.org/asterias/bzr/signs@@ ----- !! GeneSrF All the code for [[GeneSrF -> http://genesrf.bioinfo.cnio.es]]. Download it doing @@bzr get http://bioinformatics.org/asterias/bzr/genesrf@@ ----- Changed lines 111-114 from:
The rest of Asterias is not yet ready for download: we are refactoring a lot of code to make it simpler to install anywhere and it is taking longer than we thought. We will be releasing the different pieces as they become ready. to:
The rest will be available very soon. December 21, 2006, at 08:11 AM
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All the code for [[ADaCGH -> http://adacgh.bioinfo.cnio.es]]. This includes of the stand-alone ADaCGH R package. The best is for you to grab the complete sources: to:
All the code for [[ADaCGH -> http://adacgh.bioinfo.cnio.es]]. This includes the stand-alone ADaCGH R package. The best is for you to grab the complete sources: Changed lines 35-36 from:
(just in case: the version might have changed; visit the page and check it out and update if needed). to:
(the version might have changed; visit the page and check it out and update if needed). December 21, 2006, at 08:11 AM
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----- December 21, 2006, at 08:10 AM
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!! Pomelo II All the code for [[Pomelo II -> http://pomelo2.bioinfo.cnio.es]]. The C++ can be compiled for stand-alone operation. Download it doing @@bzr get http://bioinformatics.org/asterias/bzr/pomelo2@@ to:
!! Asterias common There are some installation instructions common to all Asterias web applications, scripts that might help you with the installation, LAM/MPI controlling scripts, etc. You will need this (or something similar) for all your attempts to install the web-based applications until we can finally provide a working Pylons-based egg installer. @@bzr get http://bioinformatics.org/asterias/bzr/Asterias-common@@ Added lines 23-45:
!! ADaCGH All the code for [[ADaCGH -> http://adacgh.bioinfo.cnio.es]]. This includes of the stand-alone ADaCGH R package. The best is for you to grab the complete sources: @@bzr get http://bioinformatics.org/asterias/bzr/adacgh@@ but if you only want the R package you can just do @@wget http://bioinformatics.org/asterias/bzr/adacgh/R-packages/ADaCGH_0.9-5.tar.gz@@ (just in case: the version might have changed; visit the page and check it out and update if needed). !! Pomelo II All the code for [[Pomelo II -> http://pomelo2.bioinfo.cnio.es]]. The C++ can be compiled for stand-alone operation. Download it doing @@bzr get http://bioinformatics.org/asterias/bzr/pomelo2@@ ----- October 22, 2006, at 02:48 PM
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Please note that comprehensive testing of the Javascript and AJAX functionality for Pomelo II is not included here. Instead, that testing is carried out using [[Selenium -> http://www.openqa.org/selenium/]]. See the [[Pomelo Selenium tests page -> http://pomelo2.bioinfo.cnio.es/tests.html]]. These tests have been verified with Opera (8.54) under Windows and Linux, Firefox 1.5 (Windows and Linux), Konqueror 3.5 (Linux) and Internet Explorer 1.6 (only Windows). These tests do not run under Opera 9.0 or 9.02 (something strange in the way the JS is processed by Opera). September 20, 2006, at 06:22 PM
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@@bzr get http://asterias.bioinfo.cnio.es/bzr/PomeloII@@ to:
@@bzr get http://bioinformatics.org/asterias/bzr/pomelo2@@ Changed lines 28-31 from:
@@bzr get http://asterias.bioinfo.cnio.es/bzr/Testing@@ to:
@@bzr get http://bioinformatics.org/asterias/bzr/Testing@@ Changed lines 38-40 from:
@@bzr get http://asterias.bioinfo.cnio.es/bzr/RJaCGH@@ to:
@@bzr get http://bioinformatics.org/asterias/bzr/RJaCGH@@ Changed lines 52-54 from:
@@bzr get http://asterias.bioinfo.cnio.es/bzr/varSelRF@@ to:
@@bzr get http://bioinformatics.org/asterias/bzr/varSelRF@@ September 12, 2006, at 06:29 PM
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Most of Asterias is not yet (2006-06-05) ready for download: we are refactoring a lot of code to make it simpler to install anywhere and it is taking longer than we thought. We will be releasing the different pieces as they become ready. to:
The rest of Asterias is not yet ready for download: we are refactoring a lot of code to make it simpler to install anywhere and it is taking longer than we thought. We will be releasing the different pieces as they become ready. September 12, 2006, at 06:28 PM
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!![+++ %color=#ff7f00% DownloadPage +++] to:
!! %green% Code downloads Deleted lines 6-18:
>>center<< >><< >>center<< !! %green% Downloading the code >><< September 12, 2006, at 06:27 PM
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----- September 12, 2006, at 06:26 PM
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!! Pomelo II All the code for [[Pomelo II -> http://pomelo2.bioinfo.cnio.es]]. The C++ can be compiled for stand-alone operation. Download it doing @@bzr get http://asterias.bioinfo.cnio.es/bzr/PomeloII@@ !! Functional Testing: The Python and R code for functional and regression testing. You will need [[Funkload -> http://funkload.nuxeo.org/]] for it to work. If you want to use the email reporting facilities, you will need to provide a login, password, and set of email recipients in the file /PomeloII/test_chron.py. The most recent code is available doing @@bzr get http://asterias.bioinfo.cnio.es/bzr/Testing@@ ---- Changed lines 73-87 from:
!! Functional Testing: The Python and R code for functional and regression testing. You will need [[Funkload -> http://funkload.nuxeo.org/]] for it to work. If you want to use the email reporting facilities, you will need to provide a login, password, and set of email recipients in the file /PomeloII/test_chron.py. The most recent code is available doing @@bzr get http://asterias.bioinfo.cnio.es/bzr/Testing@@ ---- ---- to:
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!! Downloading the code to:
!! %green% Downloading the code September 12, 2006, at 06:19 AM
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!! Downloading the code to:
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>>center<< !! Downloading the code >><< Added lines 48-60:
----- !! Functional Testing: The Python and R code for functional and regression testing. You will need [[Funkload -> http://funkload.nuxeo.org/]] for it to work. If you want to use the email reporting facilities, you will need to provide a login, password, and set of email recipients in the file /PomeloII/test_chron.py. The most recent code is available doing @@bzr get http://asterias.bioinfo.cnio.es/bzr/Testing@@ September 08, 2006, at 12:33 PM
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----- !! varSelRF: The R package is available from [[CRAN -> http://cran.r-project.org/src/contrib/Descriptions/varSelRF.html]] in the usual tar.gz and zip formats. The most recent code is available doing @@bzr get http://asterias.bioinfo.cnio.es/bzr/varSelRF@@ A paper that describes one of the methods implemented there is available from [[BMC Bioinformatics -> http://www.biomedcentral.com/1471-2105/7/3/abstract]]. Changed lines 42-43 from:
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>><< August 25, 2006, at 07:58 PM
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A description of the method implemented in RJaCGH is available as a [[technical report -> http://www.ligarto.org/rdiaz/Papers/rjhmm-preprint.pdf]]. to:
A description of the method implemented in RJaCGH is available as a [[COBRA Preprint Series Article -> http://biostats.bepress.com/cobra/ps/art9/]]. August 24, 2006, at 12:28 PM
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The code for the project is also mirrored at [[Launchpad -> http://launchpad.net/projects/asterias]]. August 24, 2006, at 12:21 PM
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A description of the method is available as a [[technical report -> http://www.ligarto.org/rdiaz/Papers/rjhmm-preprint.pdf]]. to:
A description of the method implemented in RJaCGH is available as a [[technical report -> http://www.ligarto.org/rdiaz/Papers/rjhmm-preprint.pdf]]. ---- Added lines 33-34:
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---- August 24, 2006, at 12:16 PM
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!! %red% Latest news Asterias is not yet (2006-06-05) ready for download: we are refactoring a lot of code to make it simpler to install anywhere and it is taking longer than we thought. We will be releasing the different pieces as they become ready. !! Requirements: to:
!! Downloading the code We use [[Bazaar-NG -> http://bazaar-vcs.org]] for version control ([[reasons why we choose Bazaar -> http://www.ligarto.org/rdiaz/VersionControl.html]]). You'll have to install Bazaar and then do @@bzr get whatever.url.we.provide@@ to get the code. Other forms might be available (e.g., tar.gz files with the R packages), but by using bzr you'll get the most recent code. Moreover, this makes it simpler to collaborate with us, send patches, etc. !! RJaCGH: The R package is available from [[CRAN -> http://cran.r-project.org/src/contrib/Descriptions/RJaCGH.html]] in the usual tar.gz and zip formats. The most recent code is available doing @@bzr get http://asterias.bioinfo.cnio.es/bzr/RJaCGH@@ A description of the method is available as a [[technical report -> http://www.ligarto.org/rdiaz/Papers/rjhmm-preprint.pdf]]. !! Other applications Most of Asterias is not yet (2006-06-05) ready for download: we are refactoring a lot of code to make it simpler to install anywhere and it is taking longer than we thought. We will be releasing the different pieces as they become ready. !! Requirements for the web-based applications: Deleted lines 51-57:
!! Downloading the code We use [[Bazaar-NG -> http://bazaar-vcs.org]] for version control ([[reasons why we choose Bazaar -> http://www.ligarto.org/rdiaz/VersionControl.html]]). You'll have to install Bazaar and then do @@bzr branch whatever.url.we.provide@@ when the repository is ready. We will also try to provide a web-based interface for the repository. June 05, 2006, at 09:40 AM
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See the [[licenses page]] for details, and the first lines of each file \ to:
See the [[LicensesPage]] for details, and the first lines of each file \ June 05, 2006, at 09:37 AM
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!![+++ %color=#ff7f00% Download page +++] to:
!![+++ %color=#ff7f00% DownloadPage +++] June 05, 2006, at 08:59 AM
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* Python 2.4 (and a bunch of Python 2.4 packages; fixme: be explicit). to:
* [[Python 2.4 -> http://www.python.org]] (and a bunch of Python 2.4 packages; fixme: be explicit). Changed lines 18-19 from:
* R (2.2.0 or higher), and several R and BioC packages (fixme: be explicit). to:
* [[R -> http://cran.r-project.org]] (2.2.0 or higher), and several R and BioC packages (fixme: be explicit). Changed lines 24-25 from:
* MPI (only tested with LAM/MPI) to:
* MPI (only tested with [[LAM/MPI -> http://www.lam-mpi.org]]) Changed lines 30-31 from:
* For load balancing and high-availability of web services: [[Linux Virtual Server -> http://www.linuxvirtualserver.org]] and [[ldirectord -> http://www.vergenet.net/linux/ldirectord/]] or [[Pound -> http://www.apsis.ch/pound/]] to:
* For load balancing and high-availability of web services: [[heartbeat -> http://www.linux-ha.org/]] and either [[Linux Virtual Server -> http://www.linuxvirtualserver.org]] and [[ldirectord -> http://www.vergenet.net/linux/ldirectord/]]) or [[Pound -> http://www.apsis.ch/pound/]] (Pound already monitors the servers). June 05, 2006, at 08:52 AM
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>>center<< !![+++ %color=#ff7f00% Download page +++] >><< !! %red% Latest news Asterias is not yet (2006-06-05) ready for download: we are refactoring a lot of code to make it simpler to install anywhere and it is taking longer than we thought. We will be releasing the different pieces as they become ready. !! Requirements: * Python 2.4 (and a bunch of Python 2.4 packages; fixme: be explicit). * A web server (only tested with Apache 1.3) * R (2.2.0 or higher), and several R and BioC packages (fixme: be explicit). * A C/C++ compiler * PHP * MPI (only tested with LAM/MPI) * Sufficient storage space for temporary files (currently project takes about 12 GB, and most of those are temporary files). * For IDconverter and IDClight about 20 GB for the pregenerated tables. * For load balancing and high-availability of web services: [[Linux Virtual Server -> http://www.linuxvirtualserver.org]] and [[ldirectord -> http://www.vergenet.net/linux/ldirectord/]] or [[Pound -> http://www.apsis.ch/pound/]] * For functional and regression testing: [[FunkLoad -> http://funkload.nuxeo.org/]] * To grab the latest code from our repositories: [[Bazaar-NG -> http://bazaar-vcs.org]] !! Downloading the code We use [[Bazaar-NG -> http://bazaar-vcs.org]] for version control ([[reasons why we choose Bazaar -> http://www.ligarto.org/rdiaz/VersionControl.html]]). You'll have to install Bazaar and then do @@bzr branch whatever.url.we.provide@@ when the repository is ready. We will also try to provide a web-based interface for the repository. !! Licenses we use for the code See the [[licenses page]] for details, and the first lines of each file \ you are interested in, since we use either the GPL or the Affero GPL. |