RPy testsuite some tests passing - enough for Galaxy?
Dear Galaxy devs, We are in the process of deploying Galaxy internally here at AgResearch, and I am currently installing required dependencies. My question relates to RPy. It seems that RPy2 is not yet supported by Galaxy, so we're stuck with RPy 1.0.3a, and this seems to have rusted quite badly. (I note however that the remarks previously made on the Galaxy lists about changes required to RPy appear to have been rolled into 1.0.3a.) After installing RPy 1.0.3a, I ran the bundled test suite. Many tests succeed, but there are several errors, in the following categories: 1. Errors about numpy, e.g. object of type numpy.int64 has no len() (Maybe numpy has changed since RPy 1.0.3a was written. I am using numpy 1.4.1 on CentOS 6.) 2. Errors due to missing files, e.g. logit.r and table.txt test data files do not appear to ship with RPy-1.0.3a (!) 3. An error in testLapackLoad, which may be because of (2), I'm not sure yet. 4. An R object index out of range error in testGetItemSlice, which looks quite serious. So here's my question. Just how much of RPy has to work, for its use in Galaxy to be OK? I attach my RPy test suite output in case anyone is (a) interested, (b) has any useful comments. cheers, Simon Simon Guest Senior UNIX Technical Consultant AgResearch, NZ ======================================================================= Attention: The information contained in this message and/or attachments from AgResearch Limited is intended only for the persons or entities to which it is addressed and may contain confidential and/or privileged material. Any review, retransmission, dissemination or other use of, or taking of any action in reliance upon, this information by persons or entities other than the intended recipients is prohibited by AgResearch Limited. If you have received this message in error, please notify the sender immediately. =======================================================================
Rpy is only used by a handful of tools (should be listed on the tool dependencies page). Everything else in Galaxy should work fine without it.
Rpy is only used by a handful of tools (should be listed on the tool dependencies page). Everything else in Galaxy should work fine without it.
Yes, I realise that. It's that handful of tools I'm interested in. I expect they will do their thing just fine with a semi-broken RPy, but I was hoping someone might be able to confirm that. Will have to test locally then. cheers, Simon ======================================================================= Attention: The information contained in this message and/or attachments from AgResearch Limited is intended only for the persons or entities to which it is addressed and may contain confidential and/or privileged material. Any review, retransmission, dissemination or other use of, or taking of any action in reliance upon, this information by persons or entities other than the intended recipients is prohibited by AgResearch Limited. If you have received this message in error, please notify the sender immediately. =======================================================================
Hi,I want learn how to use the tool "BOWtie 2",Could you tell me where can I find the tutorial? Thanks! best regards to you! dengyongyilong From: James Taylor Date: 2012-12-06 00:02 To: Guest, Simon CC: galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] RPy testsuite some tests passing - enough for Galaxy? Rpy is only used by a handful of tools (should be listed on the tool dependencies page). Everything else in Galaxy should work fine without it. ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Hi all, when I use the tool "FastQC:Read QC" I got the next index: "An error occurred running this job: Traceback (most recent call last): File "/home/galaxy/galaxy-dist/tools/rgenetics/rgFastQC.py", line 158, in assert os.path.isfile(opts.executable),'##rgFastQC.py error - cannot find executable %s' % opts.executable AssertionError: ##rgFast". Could you help me to solve this? look forward to your reply! best regards! 发件人： dengyongyilong 发送时间： 2012-12-06 09:20 收件人： James Taylor; Guest, Simon 抄送： galaxy-dev@lists.bx.psu.edu 主题： Re: Re: [galaxy-dev] RPy testsuite some tests passing - enough for Galaxy? Hi,I want learn how to use the tool "BOWtie 2",Could you tell me where can I find the tutorial? Thanks! best regards to you! dengyongyilong From: James Taylor Date: 2012-12-06 00:02 To: Guest, Simon CC: galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] RPy testsuite some tests passing - enough for Galaxy? Rpy is only used by a handful of tools (should be listed on the tool dependencies page). Everything else in Galaxy should work fine without it. ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
participants (3)
-
dengyongyilong -
Guest, Simon -
James Taylor