pathway-tools v24 has a number of improvements but is creating some issues:
1) if attempt to download articles from pubmed via eutils fails, build fails. This occurs even if Batch-PathoLogic-Download-Pubmed-Entries is set to F in ptools-init.dat
2) download can fail due to issue with proxy, or if call rate to eutils is exceeded
3) pathologic fails on the eukaryote genomes for reasons that aren't clear. since the eukaryote genomes aren't widely used outside of paprica-mt, might be time to eliminate metabolic inference for that domain. would replace with community structure analysis based on PR2. paprica-mt would still need access to the MMETSP files.
pathway-tools v24 has a number of improvements but is creating some issues: 1) if attempt to download articles from pubmed via eutils fails, build fails. This occurs even if Batch-PathoLogic-Download-Pubmed-Entries is set to F in ptools-init.dat 2) download can fail due to issue with proxy, or if call rate to eutils is exceeded 3) pathologic fails on the eukaryote genomes for reasons that aren't clear. since the eukaryote genomes aren't widely used outside of paprica-mt, might be time to eliminate metabolic inference for that domain. would replace with community structure analysis based on PR2. paprica-mt would still need access to the MMETSP files.