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bio.tools IDs in Bioconda not in bio.tools #52

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hansioan opened this issue Feb 25, 2020 · 1 comment
Open

bio.tools IDs in Bioconda not in bio.tools #52

hansioan opened this issue Feb 25, 2020 · 1 comment

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@hansioan
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Below is a list of bio.tools IDs from Bioconda recipes that do not point to any bio.tools entries. Some are fixable, case in which I added the new id in parenthesis (needs checking) and some would require adding tools to bio.tools.

bam2fasta (None)
bold-identification (None)
chorus2 (None)
extract_fasta_seq (None)
faqcs (None)
gem_mapper (gemmapper,gem3)
hla-la (None)
ivar (None)
krakenhll (None)
ksw (None)
magicblast (None)
malt (None)
malva (None)
manta9235 (manta_sv)
mgkit
miniax
mutmap
ngmerge
pgcgap
phame
piret
popera
qtlseq
roast
sepp
sepp-refgg138
sepp-refsilva128
slimm
super_distance
taxonomy_ranks
tba
wham6216 (wham-variants)
womtool
xhmm

@matuskalas
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All of these are in #23, except where explicitly stated:
(bold are additional in #23)

bam2fasta (None)
bold-identification (None)
chorus2 (None)
extract_fasta_seq (None)
faqcs (None)
gem_mapper (gemmapper,gem3)
hla-la (None) - not in #23
ispcr - Bioconda recipe macroes biotools:{{ name }} which is populated from {% set name = "ispcr" %}, also into name: {{ name }}
ivar (None)
krakenhll (None)
ksw (None)
magicblast (None)
malt (None)
malva (None)
manta9235 (manta_sv)
mgkit
miniax
mirtop (mirtop) - fixed in bio.tools! Please keep the ID in and merge into bio-tools/content.
mutmap
ngmerge
pgcgap
phame
phylocsf - still in Bioconda
pirate - Bioconda recipe macroes biotools:{{ name|lower }} which is populated from {% set name = "PIRATE" %}, also into name: {{ name|lower }}
piret
popera
qtlseq
referenceseeker - still in Bioconda
roast - not in #23. It's package multiz (multiz) that for some reason also has 3 biotools IDs stated in Bioconda: multiz, roast, and tba
sepp
sepp-refgg138
sepp-refsilva128
shark - still in Bioconda
slimm
super_distance
taxonomy_ranks
tba - not in #23. It's package multiz (multiz) that for some reason also has 3 biotools IDs stated in Bioconda: multiz, roast, and tba
thesias
wham6216 (wham-variants)
womtool
xhmm

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