Closed Surar closed 2 years ago
Hi! Thanks for creating an issue!
Two things:
1) Can you run perbase --version
to show what version got installed? (and maybe also conda list | grep perbase
)
2) It looks like you might be running on Windows based on the screenshot? Windows builds have been turned off for nearly two years at this point due to issues with rust-htslib
. So I'm betting you have a very early version of perbase. If possible I'd recommend trying to run it on a mac or linux machine.
If it is in fact windows that is the issue, I can look into re-enableing windows builds in the hopes that whatever was broken a few years ago is now fixed!
Thank you very much for your kind reply.
1-The version is (perbase 0.1.0 h740ba55_0 bioconda) 2- I’m using a university server and it is operated by CentOS Linux, I can’t download my data on my mac computer as they are patients data, however, I have installed it on mac to check what I shall get. The result of perbase –help was (zsh: exec format error: perbase).
Don’t bother yourself with the error on mac but would be so grateful if you help me getting the base-depth on the linux server.
Many thanks and best regards
Surar
From: Seth @.> Date: Wednesday, 27 April 2022 at 14:44 To: sstadick/perbase @.> Cc: Surar Al-Hashimi (PGR) @.>, Manual @.> Subject: Re: [sstadick/perbase] Can't use the base -depth function (Issue #49)
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Hi! Thanks for creating an issue!
Two things:
If it is in fact windows that is the issue, I can look into re-enableing windows builds in the hopes that whatever was broken a few years ago is now fixed!
— Reply to this email directly, view it on GitHubhttps://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fsstadick%2Fperbase%2Fissues%2F49%23issuecomment-1111022398&data=05%7C01%7Cs.o.t.al-hashimi2%40newcastle.ac.uk%7C47751518c64547c3882308da28541831%7C9c5012c9b61644c2a91766814fbe3e87%7C1%7C0%7C637866638904244306%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=2NLhUanZcM9ypmmYiOR4OcOTIeBgsGwqwPy2Rk5mKfo%3D&reserved=0, or unsubscribehttps://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fnotifications%2Funsubscribe-auth%2FAPZ4FTXR44EH2TXXTGQBTN3VHFAE5ANCNFSM5UOKVXLA&data=05%7C01%7Cs.o.t.al-hashimi2%40newcastle.ac.uk%7C47751518c64547c3882308da28541831%7C9c5012c9b61644c2a91766814fbe3e87%7C1%7C0%7C637866638904244306%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=YcCA7lCwtIJiCLFim95lXZB1rsm5st%2FKEGWWYd8FveI%3D&reserved=0. You are receiving this because you are subscribed to this thread.Message ID: @.***>
Ah, that's odd that it's not installing the correct version on centos. Can you try running conda install -c bioconda perbase=0.8.1
?
And failing that, you could possibly download the binary from the releases page and give that a try:
wget https://github.com/sstadick/perbase/releases/download/v0.8.1/perbase-linux-amd64
mv perbase-linux-amd64 perbase
chmod +x perbase
perbase --help
Thank you very much, installing the 0.8.1 version through conda was successful. Your help is so much appreciated.
Best wishes Surar
From: Seth @.> Date: Wednesday, 27 April 2022 at 15:28 To: sstadick/perbase @.> Cc: Surar Al-Hashimi (PGR) @.>, Manual @.> Subject: Re: [sstadick/perbase] Can't use the base -depth function (Issue #49)
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Ah, that's odd that it's not installing the correct version on centos. Can you try running conda install -c bioconda perbase=0.8.1?
And failing that, you could possibly download the binary from the releases page and give that a try:
wget https://github.com/sstadick/perbase/releases/download/v0.8.1/perbase-linux-amd64
mv perbase-linux-amd64 perbase
chmod +x perbase
perbase --help
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That's great new! I'll close for now but feel free to reopen if you run into any other issues 👍
HI, could you please help me with this issue, I have downloaded perbase by conda install -c bioconda perbase. but I couldn't use base-depth function. there is only one function called simple-depth and it lacks lots of option. could you please advise how can I get the base-depth? Many thanks, Surar.![perbase](https://user-images.githubusercontent.com/66306766/165476937-724cfc45-c7ed-445c-8436-6091fa20d176.PNG)