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RobiNA error in testset usage

RobiNA error in testset usage
robina error in testset usage
Answer
6/29/13 12:47 PM
After installing RobiNA on my home computer it works fine with your testset up to the point where I am using TAIR10 cds as a refence in the mapping step.

Here I get the reproducible Java error "java.io.FileNotFoundException: C:\Users\xxx\.robindata\index\TAIR10_cds_20110103_representative_gene_model.locus.fas_TRANSCRIPTOME.lengths (Das System kann den angegebenen Pfad nicht finden)" and then it starts to create an index file what makes sense but it never comes to an end even after a day on a core2duo with 2,2GHz and 4GB RAM (Win7).

Qestion1:
Is this due to fact that the path to the index file doesn't exist yet or in other words, would the index file path be created by RobiNA automatically, when it has caclulated the first one?

Question2:
Is it possible to use pre-built Index files for Bowtie from http://bowtie-bio.sourceforge.net/index.shtml also in RobiNA to circumvent the maybe time consuming indexing step?

RE: RobiNA error in testset usage
Answer
7/1/13 10:40 AM as a reply to Gerd Helftenbein.
Hi Gerd,

and thanks for your feed back. The error you are reporting seems to indicate that the index
directory does not exist. This directory is usually created during installation and that's why
RobiNA expects it to be present and writable at runtime. The directory, however, is only created
at install time and only for the user who installs RobiNA. In case you were not the installing user,
RobiNA searches the .robindata directory in vain.

A quick way to fix this would be to create a folder named ".robindata" in your home directory
(e.g. C:\Users\YOURNAME) and then create the subdirectories "mappings", "presets" and
"index". These folders don't have to contain anything, they just need to be present at runtime.

To fix the problem i have included a mechanism that checks for the presence of the data
directories at startup and creates a default directory in case the current user was not the
user who installed RobiNA - the next RobiNA build will include this fix.


Concerning your second question - Yes, you can use prebuilt indices - you just have to
make sure they were build for bowtie1 and you have to rename the files to properly identify
them for RobiNA. For example, when using a prebuilt transcriptome search index, the
files need to have the same base name, followed by "_TRANSCRIPTOME_bwtindex." and then
the rest of the original file name (usually just the name extension. In addition to that you'll
have to supply another file that contains a simple tab-separated list of all the transcripts,
their lengths and GC content organized in three columns. For the demo data set, the index files
look like this:

TAIR10_cds_20110103_representative_gene_model.locus.fas_TRANSCRIPTOME.lengths
TAIR10_cds_20110103_representative_gene_model.locus.fas_TRANSCRIPTOME_bwtindex.1.ebwt
TAIR10_cds_20110103_representative_gene_model.locus.fas_TRANSCRIPTOME_bwtindex.2.ebwt
TAIR10_cds_20110103_representative_gene_model.locus.fas_TRANSCRIPTOME_bwtindex.3.ebwt
TAIR10_cds_20110103_representative_gene_model.locus.fas_TRANSCRIPTOME_bwtindex.4.ebwt
TAIR10_cds_20110103_representative_gene_model.locus.fas_TRANSCRIPTOME_bwtindex.rev.1.ebwt
TAIR10_cds_20110103_representative_gene_model.locus.fas_TRANSCRIPTOME_bwtindex.rev.2.ebwt

I hope this answers your questions,

best greetings,
Marc

RE: RobiNA error in testset usage
Answer
7/3/13 1:57 PM as a reply to Marc Lohse.
Hi Marc,
thanks for help solving the missing index-folder problem but now i run into a new problem some steps later.
After mapping the further analysis (Design your experiment) is aborting with the error: Warnmeldung:

In normalizePath(path.expand(path), winslash, mustWork) :
path[2]="C:/Programme/RobiNA/R/library": Zugriff verweigert
Beim Start - Warnmeldungen:
1: package "methods" in options("defaultPackages") was not found
2: package 'datasets' in options("defaultPackages") was not found
....


It makes no difference if I run RobiNA as admin or after changing the attributes of the R folder. It seems to be a problem of underlying R specific for Win7 (http://r.789695.n4.nabble.com/path-reference-problems-in-R-3-0-0-td4665625.html).

Interestingly even the commandline change of attributes as admin for the above folder aborts with the message "Pfad nicht gefunden C:\Programme\RobiNA" although I can navigate into this folder and subfolders by cd and dir?!?

Any suggestions?

Gerd

RE: RobiNA error in testset usage
Answer
7/3/13 3:25 PM as a reply to Gerd Helftenbein.
Hi Gerd,

this appears to be a nasty problem - unfortunately, i cannot reproduce it on my 32bit and 64bit Windows 7
installations (both are in a Virtual Box). I am not sure whether this has any influence on the behaviour, but
could you tell me which compination of Windows 7 (32/64 bit) and Java Virtual machine you are running
on your system (Java version and "bitness").

My guess would be that the problem arises from the fact that the seemingly inconsistent permission
administration under Windows 7 is somehow choking on a situation where an administrator installed
RobiNA and a user runs it - although the permissions have been edited. Did you check whether your
command line "attrib -r" call did actually really change the permissions on the library folder? In another
context i had the same problem and no matter what i did i couldn't get rid of the "read-only" mark.

RobiNA does not necessarily have to be installed in c:\programme (a folder that is under special
"supervision" of the ever vigilant Windows ). You might as well install it in the current user's home
(e.g. C:\Users\YOURNAME\programs\RobiNA) with normal user permissions. If you then start RobiNA
as the user who installed it, it would be really weird if you did not get access to the R library folder.

I know that's not really a satisfying solution, but it might at least enable you to use RobiNA.

I hope this helps,
best greetings,
Marc