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Update sativa #44990

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merged 137 commits into from
Jan 24, 2024
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f0cd05e
Updated sativa build, incl. test case
erikrikarddaniel Dec 12, 2023
e3c687a
Update meta.yaml with new Sativa release
erikrikarddaniel Dec 27, 2023
4c6f712
Merge branch 'master' into update-sativa
erikrikarddaniel Dec 27, 2023
78eb08d
Linting
erikrikarddaniel Dec 27, 2023
afdc4c4
Update keggcharter to 1.0.2 (#44992)
BiocondaBot Dec 27, 2023
7c3d1d1
Update hictk to v0.0.5 (#44988)
robomics Dec 27, 2023
cd49b72
Update perl-minion to 10.28 (#44495)
BiocondaBot Dec 27, 2023
8a45c4e
bugfix: strand deprecated and removed in BioPython 1.82 (#44987)
DrYak Dec 27, 2023
22ed0a7
bugfix: breaking API change between ruamel.yaml 0.17.x and 0.18 (#44989)
DrYak Dec 27, 2023
f93dc7b
Update tsebra to 1.1.2.2 (#45000)
BiocondaBot Dec 28, 2023
0eb5993
Update sylph to 0.5.1 (#45001)
BiocondaBot Dec 28, 2023
6d62909
add r-misha 3.7.0 (history version) (#44981)
TTTPOB Dec 28, 2023
8398ee4
add r-misha 3.7.1 (history version) (#44984)
TTTPOB Dec 28, 2023
3601f8a
Update viguno to 0.2.0 (#44996)
BiocondaBot Dec 28, 2023
af3c532
Update annonars to 0.32.0 (#45013)
BiocondaBot Dec 28, 2023
d54b085
Fix recognizer (#45012)
iquasere Dec 29, 2023
0583b98
Update last to 1522 (#45011)
BiocondaBot Dec 29, 2023
4dc12ba
Update pcaone to 0.4.1 (#45009)
BiocondaBot Dec 29, 2023
ba88f9e
genoflu version 1.02 (#44995)
stuber Dec 29, 2023
3e747df
Update chromhmm to 1.25 (#45016)
BiocondaBot Dec 29, 2023
f5d6b55
Update ColabFold to 1.5.5 (#45008)
milot-mirdita Dec 29, 2023
005eb89
Update expam to 1.2.2.4 (#45007)
BiocondaBot Dec 29, 2023
d73ebcc
Update upimapi to 1.13.1 (#45019)
BiocondaBot Dec 29, 2023
08ddb43
Update raptor (#44952)
eseiler Dec 29, 2023
578501e
add AnnoSINE2 recipes (#44980)
liaoherui Dec 29, 2023
4879db2
Bulk (#45014)
aliciaaevans Dec 29, 2023
6e3ed17
Update deeplc to 2.2.26 (#44238)
BiocondaBot Dec 29, 2023
fe74e96
Add recipe for CellBender v0.3.0 (#45024)
mencian Dec 29, 2023
49baea5
Fix nrpys to build on python 3.8+ (#45025)
mencian Dec 30, 2023
b8779fb
Update oakvar to 2.9.83 (#45026)
BiocondaBot Dec 30, 2023
df4f00e
Update foldcomp to 0.0.6 (#45018)
BiocondaBot Dec 30, 2023
4d075ab
Update antismash-lite to 7.1.0 (#45027)
mencian Dec 30, 2023
f4db81c
Update jcvi to 1.3.9 (#45029)
BiocondaBot Dec 30, 2023
313b18c
Update recognizer to 1.10.1 (#45031)
BiocondaBot Dec 30, 2023
bf44da8
Update midsv to 0.11.0 (#45028)
BiocondaBot Dec 31, 2023
abd5f7b
Update meta.yaml (#45041)
cmkobel Jan 3, 2024
fac515c
Rebuild unitig caller for new bifrost version (#45035)
johnlees Jan 3, 2024
5a3a493
Update annosine2 build (#45033)
liaoherui Jan 3, 2024
e36c4c5
Update rasusa to 0.8.0 (#45042)
BiocondaBot Jan 3, 2024
418fbda
Update annonars to 0.33.0 (#45043)
BiocondaBot Jan 3, 2024
bf501ad
patch viroconstrictor snakemake requirements to not use version 8.x (…
florianzwagemaker Jan 3, 2024
e99ba8f
Add Deepmei version 1.0.0 recipes (#45005)
Kanglu123 Jan 3, 2024
d50e17a
Update keggcharter to 1.1.0 (#45046)
BiocondaBot Jan 3, 2024
d556ca9
Update mosca to 2.2.0 (#45054)
BiocondaBot Jan 4, 2024
9b07186
Update fgbio to 2.2.1 (#45050)
BiocondaBot Jan 4, 2024
5d54100
Update fgbio-minimal to 2.2.1 (#45051)
BiocondaBot Jan 4, 2024
71a9eff
Update viralmsa to 1.1.41 (#45047)
BiocondaBot Jan 4, 2024
c7d15ef
Update ndex2 to 3.7.0 (#45049)
BiocondaBot Jan 4, 2024
1bdd02a
Update expam to 1.2.2.5 (#45053)
BiocondaBot Jan 4, 2024
8406aac
Update bustools to 0.43.2 (#45055)
BiocondaBot Jan 4, 2024
1d73824
Update kb-python to 0.28.1 (#45056)
BiocondaBot Jan 4, 2024
c47ceb7
Update xengsort to 2.0.5 (#44888)
BiocondaBot Jan 4, 2024
4758388
Update ena-webin-cli to 6.8.0 (#45059)
BiocondaBot Jan 4, 2024
df6303c
Update zol to 1.3.17 (#45067)
BiocondaBot Jan 4, 2024
cf99e57
Update pybiolib to 1.1.1673 (#45057)
BiocondaBot Jan 4, 2024
ea2bd23
Update pybiolib to 1.1.1682 (#45072)
BiocondaBot Jan 4, 2024
37d344c
Update adam to 1.0.1 (#45069)
heuermh Jan 5, 2024
b9eb742
Update cannoli to 1.0.1 (#45070)
heuermh Jan 5, 2024
dc57e33
Update keggcharter to 1.1.1 (#45079)
BiocondaBot Jan 5, 2024
964ae0b
Update galaxy-objectstore to 23.1.4 (#45061)
BiocondaBot Jan 5, 2024
a5778f2
Update galaxy-files to 23.1.4 (#45062)
BiocondaBot Jan 5, 2024
569d13f
Update mashmap to 3.1.3 (#45064)
BiocondaBot Jan 5, 2024
17adb30
Update rosella to 0.5.3 (#45075)
BiocondaBot Jan 5, 2024
d6e6703
Update snakemake-executor-plugin-googlebatch to 0.2.0 (#45039)
BiocondaBot Jan 5, 2024
a7ee16e
Update hifihla to 0.2.3 (#45066)
BiocondaBot Jan 5, 2024
2827872
Update micom to 0.33.1 (#45071)
BiocondaBot Jan 5, 2024
3f1e5dd
Update flight-genome to 1.6.3 (#45073)
BiocondaBot Jan 5, 2024
cbb6ecd
Update bioframe to 0.6.0 (#45076)
BiocondaBot Jan 5, 2024
cd220c7
Update metdatamodel to 0.5.5 (#45082)
BiocondaBot Jan 5, 2024
56f5416
Update odgi to 0.8.4 (#45077)
BiocondaBot Jan 5, 2024
99201d0
Update nanovar to 1.5.1 (#45084)
BiocondaBot Jan 5, 2024
af69b0a
Update r-ldweaver to 1.4 (#45058)
BiocondaBot Jan 5, 2024
55a7cdc
Update ncbi-datasets-pylib to 16.1.1 (#45090)
BiocondaBot Jan 5, 2024
34d6cc9
Update dbcan to 4.1.0 (#45088)
linnabrown Jan 5, 2024
19d6750
Update perl-math-bigint to 2.003002 (#45096)
BiocondaBot Jan 7, 2024
3b83e97
Update nf-test to 0.8.3 (#45098)
BiocondaBot Jan 7, 2024
ec103fb
Update foldcomp to 0.0.7 (#45097)
BiocondaBot Jan 7, 2024
5bceb9a
Update meta.yaml (#45086)
jluebeck Jan 7, 2024
308daed
Update ltr_retriever to 2.9.8 (#45006)
BiocondaBot Jan 7, 2024
54e0e62
prodigal: include upstream patches fixing critical bugs (#45091)
0xaf1f Jan 7, 2024
9411dde
Add vcfphasesets (#45092)
marksantcroos Jan 7, 2024
25ac727
Complexcgr (#45089)
jorgeavilacartes Jan 7, 2024
f3ac820
Update ribowaltz to 2.0 (#45065)
BiocondaBot Jan 7, 2024
46538a2
Update vcf2variants (#45083)
marksantcroos Jan 7, 2024
caff19a
Update snapatac2 to 2.5.2 (#45078)
BiocondaBot Jan 7, 2024
996eb5e
Update breseq to 0.38.2 (#45103)
BiocondaBot Jan 8, 2024
54c6341
Update mitos to 2.1.6 (#45104)
BiocondaBot Jan 8, 2024
045ad72
Update harmony-pytorch to 0.1.8 (#45106)
BiocondaBot Jan 8, 2024
db70155
Update snakemake to 8.1.0 (#45108)
BiocondaBot Jan 8, 2024
037b36e
Update ltr_retriever to 2.9.9 (#45107)
BiocondaBot Jan 8, 2024
a7f0ce1
Update tn93 to 1.0.13 (#45109)
BiocondaBot Jan 8, 2024
577b95f
Update hyphy to 2.5.59 (#45111)
BiocondaBot Jan 8, 2024
c3b5108
Update pyfaidx to 0.8.0 (#45113)
BiocondaBot Jan 8, 2024
7f65759
Depend on gcc; new sha256
erikrikarddaniel Jan 8, 2024
9ca64d5
Finally a sativa recipe that puts sativa.py in PATH
erikrikarddaniel Jan 10, 2024
d185e0b
Update mitgard to 1.1 (#45101)
BiocondaBot Jan 8, 2024
29ac2c2
Update bioframe to 0.6.1 (#45120)
BiocondaBot Jan 9, 2024
316692b
Add virusrecom (#45099)
ZhijianZhou01 Jan 9, 2024
c69f9e7
bump mitos1 (#45112)
bernt-matthias Jan 9, 2024
25a47d3
Update pybiolib to 1.1.1685 (#45119)
BiocondaBot Jan 9, 2024
f2cad9e
Update ncbi-datasets-pylib to 16.1.2 (#45124)
BiocondaBot Jan 9, 2024
c1f99b2
Update das_tool to 1.1.7 (#45123)
BiocondaBot Jan 9, 2024
2183ad0
Update virusrecom to 1.1.3 (#45122)
BiocondaBot Jan 9, 2024
d28aa80
Update severus to 0.1.2 (#45135)
BiocondaBot Jan 9, 2024
23dbe73
Update virusrecom (#45130)
ZhijianZhou01 Jan 9, 2024
67ca4d3
Update hybracter to 0.5.0 (#45128)
BiocondaBot Jan 9, 2024
c0d4206
Update dnaapler to 0.5.1 (#45129)
BiocondaBot Jan 9, 2024
72567a4
Update recentrifuge to 1.13.1 (#45132)
BiocondaBot Jan 9, 2024
07ed883
Update tissuumaps to 3.2.0.3 (#45137)
BiocondaBot Jan 9, 2024
85f54be
mitos: add tests for R packages (#44971)
bernt-matthias Jan 9, 2024
5aa4846
Update kb-python to 0.28.2 (#45138)
BiocondaBot Jan 9, 2024
b83481e
Update ena-webin-cli to 6.9.0 (#45139)
BiocondaBot Jan 9, 2024
dd28474
Update r-seqmagick to 0.1.7 (#45131)
BiocondaBot Jan 9, 2024
7444bc2
Update snakefmt to 0.9.0 (#45134)
BiocondaBot Jan 9, 2024
ce25963
remove static compilation (#45141)
boukn Jan 9, 2024
ae6cf40
Update dajin2 to 0.3.6 (#45143)
BiocondaBot Jan 10, 2024
001af1d
Update jbrowse2 to 2.10.1 (#45145)
BiocondaBot Jan 10, 2024
bcbcbb7
Update ncbi-datasets-pylib to 16.2.0 (#45144)
BiocondaBot Jan 10, 2024
9564341
Add ACI (#45121)
erinyoung Jan 10, 2024
df10d83
Update ngs-chew to 0.9.0 (#45140)
BiocondaBot Jan 10, 2024
f2ae422
Update vcfpy to 0.13.7 (#45150)
BiocondaBot Jan 10, 2024
3071bf2
Merge branch 'bioconda:master' into update-sativa
erikrikarddaniel Jan 10, 2024
1ce7509
Merge branch 'bioconda:master' into update-sativa
erikrikarddaniel Jan 10, 2024
bf351da
Avoid building on OS X
erikrikarddaniel Jan 10, 2024
881e973
Merge branch 'bioconda:master' into update-sativa
erikrikarddaniel Jan 10, 2024
b3fe983
Merge branch 'master' into update-sativa
erikrikarddaniel Jan 10, 2024
07b8238
Merge branch 'master' into update-sativa
erikrikarddaniel Jan 11, 2024
8dbf85b
Merge branch 'master' into update-sativa
erikrikarddaniel Jan 15, 2024
b68ce76
Merge branch 'master' into update-sativa
erikrikarddaniel Jan 15, 2024
0cd5a2c
Merge branch 'master' into update-sativa
erikrikarddaniel Jan 15, 2024
1fb294e
Merge branch 'master' into update-sativa
erikrikarddaniel Jan 16, 2024
96706d5
Merge branch 'master' into update-sativa
erikrikarddaniel Jan 16, 2024
084c9aa
Merge branch 'master' into update-sativa
erikrikarddaniel Jan 17, 2024
029a4f3
Merge branch 'master' into update-sativa
erikrikarddaniel Jan 22, 2024
1bfd670
Merge branch 'master' into update-sativa
erikrikarddaniel Jan 23, 2024
3ee1001
Merge branch 'master' into update-sativa
erikrikarddaniel Jan 23, 2024
e84aa1b
Merge branch 'master' into update-sativa
apeltzer Jan 24, 2024
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31 changes: 5 additions & 26 deletions recipes/sativa/build.sh
Original file line number Diff line number Diff line change
Expand Up @@ -3,30 +3,9 @@
export USE_AVX=yes
export USE_AVX2=yes

case `uname` in
Darwin) export DARWIN=1;;
Linux) export DARWIN=0;;
*) echo "Unknown architecture"; exit 1;;
esac

make -C ./raxml CC="$CC"

install -d ${PREFIX}/tmp
install -d ${PREFIX}/bin

if [ $DARWIN -eq 1 ]; then
install sativa.cfg *.py ${PREFIX}
else
install -t ${PREFIX} *.py sativa.cfg
fi

# Place a symlink to sativa.py in bin/
( cd ${PREFIX}/bin; ln -s ../sativa.py . )

mkdir ${PREFIX}/raxml
cp ./raxml/raxmlHPC8* ./raxml/*.sh ${PREFIX}/raxml

cp -r ./epac ${PREFIX}
cp -r ./tests ${PREFIX}
cp -r ./example ${PREFIX}
make -C raxml

cp -r raxml ${PREFIX}/bin
cp -r epac ${PREFIX}/bin
cp *.py ${PREFIX}/bin
cp sativa.cfg ${PREFIX}/bin
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