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DaehwanKimLab / hisat2

Graph-based alignment (Hierarchical Graph FM index)
GNU General Public License v3.0
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Problem with installlation #299

Open nebilaj opened 3 years ago

nebilaj commented 3 years ago

Hello, I am having troubles installing hisat-genotype , this appears when I try to install it manually , : I n file included from hisat2_build.cpp:20: In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/iostream:37: In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/ios:215: In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__locale:14: In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/string:506: In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/string_view:175: In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__string:57: In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/algorithm:640: In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/type_traits:418: ./version:1:1: error: expected unqualified-id 2.2.1

And When I tried to install it automatically, (following the manual) only hisat2 command worked and hisatgenotype command was ' not found'. Can anyone help me? Thank in advance

chbe-helix commented 3 years ago

Hi nebilaj,

I'm sorry to see there are issues trying to dow load hisat-genotype. Could you confirm for me that hisat-genotype repo was downloaded and that hisat2 is running properly?

You should be able to run hisat2 --help in your terminal to make sure it is running.

Thanks, Chris

nebilaj commented 3 years ago

So I've tried once again to install hisat2 in a conda environment running on python 3.7. Hisat2 is working but then when I try to install hisat-genotype using this command lines :

git clone https://github.com/DaehwanKimLab/hisat-genotype.git ~/hisatgenotype cd hisatgenotype bash setup.sh -r

I have this message error when trying to run the command : hisatgenotype --help :

(python37) nebilajj@dyn903-220 ~ % hisatgenotype zsh: command not found: hisatgenotype (python37) nebilajj@dyn903-220 ~ %

chbe-helix commented 3 years ago

Hi nebilaj,

I think we know what the issue is. Please run the following code and see if it works:

git clone --recurse-submodules https://github.com/DaehwanKimLab/hisat-genotype ~/hisatgenotype
cd ~/hisatgenotype/hisat2

git checkout dev
make

cd ../

echo "export PATH=~/hisatgenotype:~/hisatgenotype/hisat2:$PATH" >> .bashrc
echo "export PYTHONPATH=~/hisatgenotype/hisatgenotype_modules:$PYTHONPATH" >> .bashrc

Make sure you change any paths or directories to fit your setup. Let me know if this corrects your issue!

Thanks, Chris

nebilaj commented 3 years ago

Hi chris, Unfortunately, it still doesn't work :/ , I have this kind of message when I try to compile with make : third_party/cpuid.h:138:14: warning: value size does not match register size specified by the constraint and modifier [-Wasm-operand-widths] : "=&r" (__eax), "=&r" (__ebx) ^ third_party/cpuid.h:132:22: note: use constraint modifier "w" "xor{l}\t{%2, %0|%0, %2}\n\t" ^~ %w0

and at the end this : `/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__config:1035:48: note: expanded from macro '_LIBCPP_DEPRECATED'

define _LIBCPP_DEPRECATED attribute ((deprecated))

                                           ^

11 warnings and 2 errors generated. make: *** [hisat2-build-s] Error 1`

so when I type hisatgenotype --help it still says

zsh: command not found: hisatgenotype

Thank you ! , Nebila

nebilaj commented 3 years ago

I tried to delete both hisat2 ( because I have also one running in my conda environment that I downloaded directly from anaconda with this line 'conda install -c bioconda hisat2' ) and when I tried to follow your step do download again hisat-genotype I can't even make hisat2 working

chbe-helix commented 3 years ago

Hi Nebila,

I think this falls into a hisat2 issue so I'm going to get you in touch with our HISAT2 team to help you with your troubles. My suggestion is to work with them to get HISAT2 in your system then head back here and I can help you get hisat-genotype working with that instillation

Thanks, Chris

parkchanhee commented 3 years ago

@nebilaj Hi Nebila, What is the OS version and the Xcode version? Is it the Apple M1 platform?

nebilaj commented 3 years ago

@nebilaj Hi Nebila, What is the OS version and the Xcode version? Is it the Apple M1 platform?

Hi! The OS version is the newest one : macOS is 11.4 and yes I am running on M1 platform , is it the problem? thank you!

parkchanhee commented 3 years ago

The HISAT2 2.2.1 doesn't support Apple M1 platform. The HISAT2 uses special instructions of x86_64(Intel 64bit) architecture, so you couldn't compile the code on the M1 platform.

Currently, we're developing to support M1 platform(also other platforms), next release of HISAT2 may support it.

nebilaj commented 3 years ago

oh I see, so there is no way I can make it work? even using rosetta? thank you very much

parkchanhee commented 3 years ago

You can download the HISAT2 binary for Mac(Intel CPU), but we haven't tested with the Rosetta.

https://daehwankimlab.github.io/hisat2/download/#version-hisat2-221

nebilaj commented 3 years ago

Do you mean this version? OSX_x86_64 | https://cloud.biohpc.swmed.edu/index.php/s/hisat2-210-OSX_x86_64/download is it going to work on my m1 macbook? I dont have a mac intel :/