Can't use the base -depth function

[Surar]

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.

[sstadick]

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!

[Surar]

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:

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!

— 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: @.***>

[sstadick]

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

[Surar]

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

— 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-1111072967&data=05%7C01%7Cs.o.t.al-hashimi2%40newcastle.ac.uk%7C48eca1b916c24536717d08da285a269f%7C9c5012c9b61644c2a91766814fbe3e87%7C1%7C0%7C637866664900627097%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=eL7eWUznKuMMqUL4CZ2g8QVQqUgqvGJHDy0JUbZckvg%3D&reserved=0, or unsubscribehttps://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fnotifications%2Funsubscribe-auth%2FAPZ4FTTCXU7QZ666BUBSBL3VHFFHPANCNFSM5UOKVXLA&data=05%7C01%7Cs.o.t.al-hashimi2%40newcastle.ac.uk%7C48eca1b916c24536717d08da285a269f%7C9c5012c9b61644c2a91766814fbe3e87%7C1%7C0%7C637866664900783337%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=o7YQtgjejDZeo6z0T5Z5e71dYbrnQmvkEYJMFHjNibA%3D&reserved=0. You are receiving this because you are subscribed to this thread.Message ID: @.***>

[sstadick]

That's great new! I'll close for now but feel free to reopen if you run into any other issues 👍