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Install instructions #3

Closed ngiangre closed 7 years ago

ngiangre commented 7 years ago

Once I clone the repo, how do I install from there?

aboshkin commented 7 years ago

Currently, the way to build/install is:

(assuming you are in the ngs-tools directory, ngs and ncbi-vdb are cloned at the same level as ngs-tools, i.e. the parent directory has 3 subdirs, ngs, ncbi-vdb and ngs-tools)

./configure --prefix=

# add --with-debug for debug version

cd build/cmake

./makerelease.sh # or ./makedebug.sh if debug

cd Release

make all install

We are currently working on simplifying the build procedure for this repo; the plan is to have "./configure && make install" work out of the box.

kwrodarmer commented 7 years ago

@ngiangre - did that address your question?

ngiangre commented 7 years ago

I'm in a hackathon with ben busby downstairs right now but I'll get back to this issue within a day. Sorry!

ngiangre commented 7 years ago

I am configuring within ngs-tools but it can't locate ngs-sdk which is ../ngs/ngs-sdk and not within nfs-tools. How can I trace errors myself? I added the debug flag but I get the same verbose output as without

kwrodarmer commented 7 years ago

try putting ngs, ncbi-vdb and ngs-tools all at the same level (and for that matter, sra-tools). That's the most common arrangement. Remember the configure steps.

ngiangre commented 7 years ago

Yes I have ngs, ngs-tools, ncbi-vdb and sra-tools all at the same level and I'm trying to configure once I'm in ngs-tools, but when it checks for the ngs-sdk package it can't find it. It's in ../ngs/ but the configuration fails.

aboshkin commented 7 years ago

Can you post the output of the ./configure command (in ngs-tools)?

ngiangre commented 7 years ago

Nicholass-MacBook-Pro-2:ngs-tools nickgiangreco$ ./configure --with-debug Configuring NGS-TOOLS package checking system type... Darwin checking machine architecture... x86_64 build architecture: x86_64 checking for supported architecture... x86_64 (64 bits) is supported checking for supported OS... Darwin (mac) is supported checking for supported tool chain... clang tool chain is supported checking for clang++... yes checking for ngs-sdk package... includes... ../ngs/ngs-sdk configure: error: required ngs-sdk package not found.

klymenko commented 7 years ago

Here is the correct sequence of commands:

mkdir ~/SRC ; cd ~/SRC git clone https://github.com/ncbi/ngs.git git clone https://github.com/ncbi/ncbi-vdb.git git clone https://github.com/ncbi/ngs-tools.git cd ngs/ngs-sdk ; ./configure -p=~/NCBI && make cd ../../ncbi-vdb ; ./configure -p=~/NCBI && make cd ../ngs-tools ; ./configure -p=~/NCBI

kwrodarmer commented 7 years ago

He can also run the first configure within ngs itself, rather than ngs/ngs-sdk, right?

klymenko commented 7 years ago

He can also run the first configure within ngs itself, rather than ngs/ngs-sdk, right?

Yes he can - if he has java and python installed.

kwrodarmer commented 7 years ago

Yes, @ngiangre - you're writing Python code, correct?

aboshkin commented 7 years ago

Yes. ./configure from ngs/ will also configure Java and Python.

From: kwrodarmer [notifications@github.com] Sent: Thursday, March 23, 2017 11:35 AM To: ncbi/ngs-tools Cc: Boshkin, Anatoly (NIH/NLM/NCBI) [C]; Comment Subject: Re: [ncbi/ngs-tools] Install instructions (#3)

He can also run the first configure within ngs itself, rather than ngs/ngs-sdk, right?

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ngiangre commented 7 years ago

Thank you @klymenko, that worked. I will be writing python code. I'm trying to get count data for ChIPSeq experiments in HEK293 cells. And I have genomic windows in a bed file-can I convert that into a gtf file to use spark_genes tools or can I use the bed file directly?

kwrodarmer commented 7 years ago

We have no built-in support for bed files. Ben may have some feedback for you.

ngiangre commented 7 years ago

Alright, no worries. I’m sure there’s a bed to gtf conversion tool.

From: kwrodarmer notifications@github.com Reply-To: ncbi/ngs-tools reply@reply.github.com Date: Thursday, March 23, 2017 at 12:20 PM To: ncbi/ngs-tools ngs-tools@noreply.github.com Cc: Nick Giangreco nick.giangreco@gmail.com, Mention mention@noreply.github.com Subject: Re: [ncbi/ngs-tools] Install instructions (#3)

We have no built-in support for bed files. Ben may have some feedback for you.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub, or mute the thread.

ngiangre commented 7 years ago

Thanks for all your help! I'll open a new issue if I have a problem.

nroak commented 7 years ago

Can you please put these instructions on the homepage, Readme.md?

Here is the correct sequence of commands:

mkdir \~/SRC ; cd \~/SRC git clone https://github.com/ncbi/ngs.git git clone https://github.com/ncbi/ncbi-vdb.git git clone https://github.com/ncbi/ngs-tools.git cd ngs/ngs-sdk ; ./configure -p=\~/NCBI && make cd ../../ncbi-vdb ; ./configure -p=\~/NCBI && make cd ../ngs-tools ; ./configure -p=\~/NCBI

ngiangre commented 7 years ago

@nroak, I made a pull request. Thank you for your comment! This is extremely useful for easier adoption by other users.

tardigradus commented 3 years ago

It's 2021 and the correct build instructions still haven't made it into the README.de :-(