http://www.openscience.org/links/index.php?section=214
and vlinux(very old but provides another package list):
VLinux Bioinformatics workbench is a Linux distribution for Bioinformatics. It is easy to use, no installation required, CD-based distribution based on Knoppix 3.3. It includes a variety of sequence and structure analysis packages.It is an Open source product released under the GNU GPL License.
“Maven” is supposed to get dependencies using sources specified “pom.xml”. However, should the sources change, the process is likely to fail:
==================
[ERROR] BUILD ERROR [INFO] ------------------------------------------------------------------------ [INFO] Error building POM (may not be this project's POM). Project ID: org.apache.maven.plugins:maven-site-plugin Reason: POM 'org.apache.maven.plugins:maven-site-plugin' not found in repository: Unable to download the artifact from any repository org.apache.maven.plugins:maven-site-plugin:pom:2.0-beta-6
==================
The building of this package may just become a hit/miss affair.
The full log of the build is available here :
http://launchpadlibrarian.net/16935335/buildlog_ubuntu-intrepid-i386.geoserver_1.6.4b-1_FAILEDTOBUILD.txt.gz
Using “maven” to build “geoserver” to a very long time. The biggest lag seems to be in getting the dependencies.
===============================================[INFO] [compiler:compile]
[INFO] Compiling 109 source files to /home/mixo/prj/scubuntu/packages/geos/geoserver-1.6.4b/geoserver/web/target/classes
[INFO]
[INFO]
[INFO] ————————————————————————
[INFO] Reactor Summary:
[INFO] ————————————————————————
[INFO] GeoServer 1.6.4 ………………………………… SUCCESS [2:14.165s]
[INFO] GeoServer Maven Plugins …………………………. SUCCESS [0.019s]
[INFO] Plugins configuration files ……………………… SUCCESS [51:53.249s]
[INFO] Configuration Deployment PlugIn ………………….. SUCCESS [14:17.302s]
[INFO] Core Platform Module ……………………………. SUCCESS [2:06.180s]
[INFO] Data Module ……………………………………. SUCCESS [13:17.603s]
[INFO] Open Web Service Model ………………………….. SUCCESS [2.171s]
[INFO] Open Web Service Module …………………………. SUCCESS [4:33.790s]
[INFO] Main Module ……………………………………. SUCCESS [21:51.633s]
[INFO] Web Coverage Service Module ……………………… SUCCESS [4:23.036s]
[INFO] Validation Module ………………………………. SUCCESS [1.806s]
[INFO] Web Feature Service Model ……………………….. SUCCESS [2.123s]
[INFO] Web Feature Service Module ………………………. SUCCESS [2:11.920s]
[INFO] Versioning Web Feature Service Model ……………… SUCCESS [1.398s]
[INFO] Versioned Web Feature Service Module ……………… SUCCESS [2:20.017s]
[INFO] Web Map Service Module ………………………….. SUCCESS [12:22.371s]
[INFO] Web Application Module ………………………….. SUCCESS [3:45.540s]
[INFO] ————————————————————————
[INFO] ————————————————————————
[INFO] BUILD SUCCESSFUL
[INFO] ————————————————————————
[INFO] Total time: 135 minutes 25 seconds
[INFO] Finished at: Tue Aug 19 12:28:03 SAST 2008
[INFO] Final Memory: 29M/63M
[INFO] ————————————————————————
===============================================
Creating a PPA of this package should hopefullt be quicker that 2 hours plus 15 minutes.
While trying to build “geoserver” which uses the Java build tool “maven”, I came across this great use error message:
======================================================
[INFO] Scanning for projects…
[INFO] ————————————————————————
[ERROR] FATAL ERROR
[INFO] ————————————————————————
[INFO] Error building POM (mat be this project’s POM).
Project ID: unknown
Reason: Could not find the model file ‘/home/mixo/prj/scubuntu/packages/geos/geoserver-1.6.4b/geoserver/maven/pom.xml’. for project unknown
[INFO] ————————————————————————
[INFO] Trace
org.apache.maven.reactor.MavenExecutionException: Could not find the model file ‘/home/mixo/prj/scubuntu/packages/geos/geoserver-1.6.4b/geoserver/maven/pom.xml’. for project unknown
at org.apache.maven.DefaultMaven.getProjects(DefaultMaven.java:376)
at org.apache.maven.DefaultMaven.doExecute(DefaultMaven.java:289)
at org.apache.maven.DefaultMaven.execute(DefaultMaven.java:126)
at org.apache.maven.cli.MavenCli.main(MavenCli.java:282)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
.
.
.
======================================================
Now for the useful bit: there was a “module” speficied in “pom.xml” called “community”. All this made me revisit the following usel links
While trying to build signed source for “openlayers”, I get
———————
Now signing changes and any dsc files…
signfile openlayer_2.6-1.dsc Mixo Shiburi <mixo@mixo-laptop>
gpg: skipped “Mixo Shiburi <mixo@mixo-laptop>”: secret key not available
gpg: [stdin]: clearsign failed: secret key not available
debsign: gpg error occurred! Aborting….
debuild: fatal error at line 1174:
running debsign failed
——————–
I am not sure what caused the problem, I would appriciate a direction for the solution.
I have posted a rough guide to creating a PPA on the Scubuntu Wiki : http://scubuntu.meraka.org.za/wiki/Development
This is a “rough” guide, but it will be updated as more packaging is done for Scubuntu. Please update the “guide” as you see fit.
Neeshal and I were given a huge responsibility with regards to identifying the new or already existing software and packages of several scientific disciplines. I must say that we as the only ladies (P.S didn’t mean to sound sexist) within the Scubuntu group managed to handle the task pretty well. One would think that there isn’t much Open Source tools/applications/software available out there, but you will be surprised at the amount of OSS applications available. To find out how much effort we’ve put into this task please visit our Scubuntu website on:
http://scubuntu.meraka.org.za/wiki/Scientific_Software
and you are most welcomed to comment on the work that we’ve completed thus far.
While in France on our recent trip to Europe, Hennie and I met with Didier Halgand and Habib Jreige of SciLab at their offices at INRIA in Versailles.
SciLab is an open source platform for numerical computation developed at INRIA. They have a number of consortium members from industry and academic organisations, ranging from small companies to large motor manufacturers and universities.
The discussion with SciLab revolved around their business and sustainability model; this is something that needs to be considered for scubuntu as well. Their model comprises 3 stages:
There was much enthusiasm for SciLab to be included in scubuntu.
An important question that was raised was whether scubuntu would focus only on researchers, or also on engineering and industry. Focusing only on academic users proved problematic for SciLab, while including industry allowed for a more sustainable business model. This is something that needs to be considered, especially in light of (in some fields) a blurring of the line separating the two.
Partly because Mandriva is a SciLab consortium member, there was a question about how open scubuntu would be to other Linux distributions. We reassured them that all scubuntu work will be released as OSS, and will be usable in other distribution.
Hennie and I, on the Dutch leg of our recent trip abroad, visited Daan Velthausz at the SURF offices in Utrecht.
SURF is the collaborative organisation for higher education institutions and research institutes aimed at breakthrough innovations in ICT. SURF provides the foundation for the excellence of higher education and research in the Netherlands.
The scubuntu project was presented to employees working on various projects within SURF. Most of them are users of Linux and/or OSS. An important issue that was raised by a number of them was how to market scubuntu to wealthy institutions in Europe – for those institutions, cost is not a factor, and other benefits such as security, stability, speed and customisability have to be stressed.
Although there is no obvious opportunity to collaborate with SURF directly, we will keep discussions with them open. There is also the possibility of gaining access to their large customer base as possible users of and contributors to the project.
Hennie and I, on our recent trip to the UK and Europe, were taken by Michael to meet with Dr Mike Rodd , Director of the learned society & external relations for the British Computer Society (BCS), and with Paul Adams, chairman of the open Source Specialist Group of the BCS.
The BCS has approx. 70,000 members from across ICT industry in UK (incl. universities). They work with accredited international universities, including University of Johannesburg and University of Cape Town. They also have links with the Computer Society of South Africa.
Some of the problems that scubuntu will address were discussed and included:
A further problem identified with the adoption of OSS in universities in the UK is that their procurement and IT policies make it difficult to use software without a support contract. This is more of a problem in the newer universities that focus more on technology, while older research-focused universities struggle less with this.
There was a discussion about the target audience of scubuntu, and the most appropriate distribution media for each group. In the UK, connectivity is not an issue for research institutions, so a network0based installer is appropriate. In Africa, connectivity is problematic, so a CD-based installer is better.
An important issue was raised around branding and ownership of the project. For the project to be successful as a community-driven initiative, it shouldn’t be seen as a CSIR/Meraka/DST owned project. This is completely in alignment with my goals for the project - I see it as a global, open initiaive, not as being owned by Meraka. It was suggested that a statement stating (for Meraka-paid contributors) that the “CSIR supports my time on this project and acts as a beta test site” would be appropriate.
Paul Adams offered to speak to his contacts at Canonical, to request a formal statement of unofficial support for the project (e.g. a posting on the SABDFL’s weblog). He also offered to help us in finding domain specialists with IT knowledge who can contribute to the project.
A discussion about possible a exchange programme for the project led to the suggestion that we target postdocs for such a programme. The feeling was that in the UK postdocs, who tend to not yet have full time employment, would have fewer immediate demands on their time, and would be more amenable to such an exchange.
Developer sprints were suggested as the most appropriate mechanism for getting developers together and for solving specific technical challenges on scubuntu. Paul Adams has had success in the past in securing financial support from the NLNET foundation in the Netherlands for such developer sprints. Attendance of the six-monthly UDS was identified as critical for the scubuntu project. The next UDS takes place in Decmeber.
Paul Adams is willing, via his employer (Sirius Corporation) to partner with us and lead the application for EU FP7 funding.
There was a suggestion that we contact Tony Roberts, who is involved with Computer Aid in distributing refurbished machines to schools in Africa (not in SA). There may be an opportunity to include scubuntu on their machines.
Possible collaborators that were identified:
The OSS specialist group meets monthly, and can be used to spread the word about the project. There was also an invitation to present on the project at a future meeting, and to host a workshop to discuss some specific problem/challenge. In addition, the BCS is willing to send out a one-pager information document to all their members on the project.