diff --git a/tools/mitoz_annotate/mitoz_annotate.yaml b/tools/mitoz_annotate/mitoz_annotate.yaml index b17ec9fd38e1e719366e8c53c1dc99c64a47809f..54df51736e2b0d14b632e29394ed970102a69e04 100755 --- a/tools/mitoz_annotate/mitoz_annotate.yaml +++ b/tools/mitoz_annotate/mitoz_annotate.yaml @@ -158,7 +158,8 @@ "python3 -c \"from ete3 import NCBITaxa;ncbi = NCBITaxa();ncbi.update_taxonomy_database()\"", "sed -i 's/^ yield rec/ try:\n yield rec/' /opt/biotools/release_MitoZ_v2.4-alpha/bin/annotate/gene_feature.py ", "sed -i 's/^ raise StopIteration/ except:\n raise StopIteration/' /opt/biotools/release_MitoZ_v2.4-alpha/bin/annotate/gene_feature.py ", - "# see https://docs.python.org/3/whatsnew/3.7.html#changes-in-python-behavior" + "# see https://docs.python.org/3/whatsnew/3.7.html#changes-in-python-behavior ", + "sed 's/#return re.sub(pos_old, pos_new, str(pos))/return pos_new/' /opt/biotools/release_MitoZ_v2.4-alpha/bin/common/genbank_gene_stat_v2.py" ], ncbi_tools: [ #tbl2asn "apt-get install -y ncbi-tools-bin" diff --git a/tools/mitoz_assemble/mitoz_assemble.yaml b/tools/mitoz_assemble/mitoz_assemble.yaml index c761795d5ed261ec09c240bf789ad11cea7ed4a2..0f7fc4b30a6110ca81aae17dfe98b358fd675d4f 100755 --- a/tools/mitoz_assemble/mitoz_assemble.yaml +++ b/tools/mitoz_assemble/mitoz_assemble.yaml @@ -177,7 +177,9 @@ "python3 -c \"from ete3 import NCBITaxa;ncbi = NCBITaxa();ncbi.update_taxonomy_database()\"", "sed -i 's/^ yield rec/ try:\n yield rec/' /opt/biotools/release_MitoZ_v2.4-alpha/bin/annotate/gene_feature.py ", "sed -i 's/^ raise StopIteration/ except:\n raise StopIteration/' /opt/biotools/release_MitoZ_v2.4-alpha/bin/annotate/gene_feature.py ", - "# see https://docs.python.org/3/whatsnew/3.7.html#changes-in-python-behavior" + "# see https://docs.python.org/3/whatsnew/3.7.html#changes-in-python-behavior", + "sed 's/#return re.sub(pos_old, pos_new, str(pos))/return pos_new/' /opt/biotools/release_MitoZ_v2.4-alpha/bin/common/genbank_gene_stat_v2.py" + ] }, citations: { diff --git a/tools/mitoz_filter/mitoz_filter.yaml b/tools/mitoz_filter/mitoz_filter.yaml index dda48cdfdc843434b816bc0aed923ecf9e4b9665..07b72619edc56d4e30b6bbf7eae039b9422a7671 100755 --- a/tools/mitoz_filter/mitoz_filter.yaml +++ b/tools/mitoz_filter/mitoz_filter.yaml @@ -186,7 +186,9 @@ "python3 -c \"from ete3 import NCBITaxa;ncbi = NCBITaxa();ncbi.update_taxonomy_database()\"", "sed -i 's/^ yield rec/ try:\n yield rec/' /opt/biotools/release_MitoZ_v2.4-alpha/bin/annotate/gene_feature.py ", "sed -i 's/^ raise StopIteration/ except:\n raise StopIteration/' /opt/biotools/release_MitoZ_v2.4-alpha/bin/annotate/gene_feature.py ", - "# see https://docs.python.org/3/whatsnew/3.7.html#changes-in-python-behavior" + "# see https://docs.python.org/3/whatsnew/3.7.html#changes-in-python-behavior", + "sed 's/#return re.sub(pos_old, pos_new, str(pos))/return pos_new/' /opt/biotools/release_MitoZ_v2.4-alpha/bin/common/genbank_gene_stat_v2.py" + ] }, citations: { diff --git a/tools/mitoz_findmitoscaf/mitoz_findmitoscaf.yaml b/tools/mitoz_findmitoscaf/mitoz_findmitoscaf.yaml index cae4a16c6be1f32f6114404870fc184613665a85..d166c890dc8f85d670244fde7c2f0ad7f79da1a9 100755 --- a/tools/mitoz_findmitoscaf/mitoz_findmitoscaf.yaml +++ b/tools/mitoz_findmitoscaf/mitoz_findmitoscaf.yaml @@ -106,7 +106,9 @@ "python3 -c \"from ete3 import NCBITaxa;ncbi = NCBITaxa();ncbi.update_taxonomy_database()\"", "sed -i 's/^ yield rec/ try:\n yield rec/' /opt/biotools/release_MitoZ_v2.4-alpha/bin/annotate/gene_feature.py ", "sed -i 's/^ raise StopIteration/ except:\n raise StopIteration/' /opt/biotools/release_MitoZ_v2.4-alpha/bin/annotate/gene_feature.py ", - "# see https://docs.python.org/3/whatsnew/3.7.html#changes-in-python-behavior" + "# see https://docs.python.org/3/whatsnew/3.7.html#changes-in-python-behavior", + "sed 's/#return re.sub(pos_old, pos_new, str(pos))/return pos_new/' /opt/biotools/release_MitoZ_v2.4-alpha/bin/common/genbank_gene_stat_v2.py" + ] }, citations: {