Upgrading My Local Galaxy Install

Question: Upgrading My Local Galaxy Install

9.4 years ago by

Erick Antezana • 570 wrote:

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

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modified 9.4 years ago • written 9.4 years ago by Erick Antezana • 570

9.4 years ago by

Erick Antezana • 570

Erick Antezana • 570 wrote:

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>

ADD COMMENT • link written 9.4 years ago by Erick Antezana • 570

Hi Erick, This message should be safe to ignore. Galaxy still supports Python 2.4. This is most likely the case. You can view the output for the error to see if this is not the case, but for most tools, the problem is usually a missing dependency. If you don't use those tools, the error can be safely ignored. Eggs are updated automatically by the framework. It can also be done manually with the 'fetch_eggs.py' script in Galaxy's 'scripts/' directory. --nate

ADD REPLY • link written 9.4 years ago by Nate Coraor ♦ 3.2k

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