From cb308620d60a7ad905de00c7f90527dabaa6d988 Mon Sep 17 00:00:00 2001 From: paulzierep Date: Wed, 5 Jun 2024 10:33:29 +0200 Subject: [PATCH] use TSV --- bin/extract_galaxy_tools.py | 2 +- bin/get_public_galaxy_servers.py | 2 +- data/available_public_servers.csv | 78 +++++++++++++++---------------- 3 files changed, 41 insertions(+), 41 deletions(-) diff --git a/bin/extract_galaxy_tools.py b/bin/extract_galaxy_tools.py index 971a9fd4..55ebe72e 100644 --- a/bin/extract_galaxy_tools.py +++ b/bin/extract_galaxy_tools.py @@ -740,7 +740,7 @@ def reduce_ontology_terms(terms: List, ontology: Any) -> List: tool[f"Tools available on {name}"] = check_tools_on_servers(tool["Galaxy tool ids"], url) # add all other available servers - public_servers_df = pd.read_csv(public_servers) + public_servers_df = pd.read_csv(public_servers, sep="\t") for index, row in public_servers_df.iterrows(): name = row["name"] diff --git a/bin/get_public_galaxy_servers.py b/bin/get_public_galaxy_servers.py index 7b222ddf..a8c66df8 100644 --- a/bin/get_public_galaxy_servers.py +++ b/bin/get_public_galaxy_servers.py @@ -48,7 +48,7 @@ def get_public_galaxy_servers(output: str) -> None: s = pd.Series(to_process) s.index.name = "name" s.name = "url" - s.to_csv(output) + s.to_csv(output, sep="\t") if __name__ == "__main__": diff --git a/data/available_public_servers.csv b/data/available_public_servers.csv index 487d7b85..a4947360 100644 --- a/data/available_public_servers.csv +++ b/data/available_public_servers.csv @@ -1,39 +1,39 @@ -name,url -ANASTASIA,http://motherbox.chemeng.ntua.gr/anastasia_dev/ -APOSTL,http://apostl.moffitt.org/ -ARGs-OAP,http://smile.hku.hk/SARGs -BF2I-MAP,http://bf2i-galaxy.insa-lyon.fr:8080/ -BioBix,http://galaxy.ugent.be/ -CIRM-CFBP,https://iris.angers.inra.fr/galaxypub-cfbp -Center for Phage Technology (CPT),https://cpt.tamu.edu/galaxy-public/ -ChemFlow,https://vm-chemflow-francegrille.eu/ -Coloc-stats,https://hyperbrowser.uio.no/coloc-stats -CorGAT,http://corgat.cloud.ba.infn.it/galaxy -CropGalaxy,http://cropgalaxy.excellenceinbreeding.org/ -Dintor,http://dintor.eurac.edu/ -FreeBioinfo,http://www.freebioinfo.org/ -GASLINI,http://igg.cloud.ba.infn.it/galaxy -Galaxy@AuBi,https://galaxy.mesocentre.uca.fr -Galaxy@Pasteur,https://galaxy.pasteur.fr/ -GalaxyTrakr,https://galaxytrakr.org/ -Genomic Hyperbrowser,http://hyperbrowser.uio.no/hb/ -GigaGalaxy,http://gigagalaxy.net/ -HyPhy HIV NGS Tools,https://galaxy.hyphy.org/ -IPK Galaxy Blast Suite,https://galaxy-web.ipk-gatersleben.de -ImmPort Galaxy,https://www.immportgalaxy.org/ -InteractoMIX,http://galaxy.interactomix.com/ -MISSISSIPPI,https://mississippi.sorbonne-universite.fr -Mandoiu Lab,https://neo.engr.uconn.edu/ -MiModD NacreousMap,http://mapping-by-sequencing.vm.uni-freiburg.de:8080/ -Oqtans,http://galaxy.inf.ethz.ch -Palfinder,https://palfinder.ls.manchester.ac.uk/ -PepSimili,http://pepsimili.e-nios.com:8080/ -PhagePromotor,https://galaxy.bio.di.uminho.pt/ -Protologger,http://protologger.de/ -UseGalaxy.be,https://usegalaxy.be/ -UseGalaxy.cz,https://usegalaxy.cz/ -UseGalaxy.eu,https://usegalaxy.eu -UseGalaxy.fr,https://usegalaxy.fr/ -UseGalaxy.no,https://usegalaxy.no/ -UseGalaxy.org (Main),https://usegalaxy.org -UseGalaxy.org.au,https://usegalaxy.org.au +name url +ANASTASIA http://motherbox.chemeng.ntua.gr/anastasia_dev/ +APOSTL http://apostl.moffitt.org/ +ARGs-OAP http://smile.hku.hk/SARGs +BF2I-MAP http://bf2i-galaxy.insa-lyon.fr:8080/ +BioBix http://galaxy.ugent.be/ +CIRM-CFBP https://iris.angers.inra.fr/galaxypub-cfbp +Center for Phage Technology (CPT) https://cpt.tamu.edu/galaxy-public/ +ChemFlow https://vm-chemflow-francegrille.eu/ +Coloc-stats https://hyperbrowser.uio.no/coloc-stats +CorGAT http://corgat.cloud.ba.infn.it/galaxy +CropGalaxy http://cropgalaxy.excellenceinbreeding.org/ +Dintor http://dintor.eurac.edu/ +FreeBioinfo http://www.freebioinfo.org/ +GASLINI http://igg.cloud.ba.infn.it/galaxy +Galaxy@AuBi https://galaxy.mesocentre.uca.fr +Galaxy@Pasteur https://galaxy.pasteur.fr/ +GalaxyTrakr https://galaxytrakr.org/ +Genomic Hyperbrowser http://hyperbrowser.uio.no/hb/ +GigaGalaxy http://gigagalaxy.net/ +HyPhy HIV NGS Tools https://galaxy.hyphy.org/ +IPK Galaxy Blast Suite https://galaxy-web.ipk-gatersleben.de +ImmPort Galaxy https://www.immportgalaxy.org/ +InteractoMIX http://galaxy.interactomix.com/ +MISSISSIPPI https://mississippi.sorbonne-universite.fr +Mandoiu Lab https://neo.engr.uconn.edu/ +MiModD NacreousMap http://mapping-by-sequencing.vm.uni-freiburg.de:8080/ +Oqtans http://galaxy.inf.ethz.ch +Palfinder https://palfinder.ls.manchester.ac.uk/ +PepSimili http://pepsimili.e-nios.com:8080/ +PhagePromotor https://galaxy.bio.di.uminho.pt/ +Protologger http://protologger.de/ +UseGalaxy.be https://usegalaxy.be/ +UseGalaxy.cz https://usegalaxy.cz/ +UseGalaxy.eu https://usegalaxy.eu +UseGalaxy.fr https://usegalaxy.fr/ +UseGalaxy.no https://usegalaxy.no/ +UseGalaxy.org (Main) https://usegalaxy.org +UseGalaxy.org.au https://usegalaxy.org.au