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