Hi, sorry for insisting on this, I just would like to have a confirmation about the upgrading procedure... Are those steps sufficient? thanks Erick 2009/6/30 Erick Antezana <erick.antezana@gmail.com>

Hi,

I have upgraded my local install by getting the latest source like this:

hg pull -u

then I compared the *.sample.xml files against my *.xml files (tool_conf.xml).

I have also upgraded my DB (from version 6 to 7).

I have also launched :

sh run_functional_tests.sh

and I got a message:

... *** This program requires python version 2.5 or higher *** Current python version is: 2.4.3.final.0 ...

I have python 2.4.3. Do I need to upgrade it?

During the tests execution I saw the following error messages:

... Test uploading encode data ... ERROR ... ... Gencode Partition ( gencode_partition1 ) > Test-1 ... FAIL ... Stitch MAF blocks ( Interval_Maf_Merged_Fasta2 ) > Test-1 ... FAIL Stitch MAF blocks ( Interval_Maf_Merged_Fasta2 ) > Test-2 ... FAIL ... Summary Statistics ( Summary_Statistics1 ) > Test-1 ... FAIL ... BLAT ( blat_wrapper ) > Test-1 ... FAIL ... Fetch taxonomic representation ( Fetch Taxonomic Ranks ) > Test-1 ... FAIL Poisson two-sample test ( poisson2test ) > Test-1 ... FAIL Poisson two-sample test ( poisson2test ) > Test-2 ... FAIL Compute phastOdds score ( phastOdds_for_intervals ) > Test-1 ... FAIL LAV to BED ( lav_to_bed1 ) > Test-1 ... FAIL ... FAILED (failures=38, errors=5)

the rest are OK, some errors and failures I guess are due to the fact that I do not have some tools installed (e.g. BLAT)

Do I need to perform any other operation in order to upgrate my local install? (what about the "eggs"? Do I need to check for egg updates? how?)

thanks, Erick