Comments (18)
Hi Zhijian,
I followed the last instructions and HINT is working perfectly fine on M1 Mac. Thanks again so much for your help.
from reg-gen.
Hi,
Could you show how you install the package on M1 Mac and the version of RGT?
You can get the version information by rgt-hint --version
from reg-gen.
Hi Zhijian
I tried to install using the generic approach here [https://github.com/CostaLab/reg-gen].
I have also used the Mac-specific approach described in your website here: [https://reg-gen.readthedocs.io/en/latest/rgt/installation.html]:
I have RGT installed in my Intel Mac and it runs fine. I would like to install on the M1 Macs in my lab for my postdocs and students to use it.
Thanks a lot again for your help,
Ricardo
from reg-gen.
from reg-gen.
Hi,
The latest version of develop branch is v1.0.1.
Can you try to install it from the source code?
To do so, you need to run the following commands:
[email protected]:CostaLab/reg-gen.git
git checkout develop
pip install ./
Please let me know if this fixes the issue on m1.
from reg-gen.
When I do this it just reinstalls the 1.0.0 version. I downloaded from the 'develop' branch here
After I install and run i get the same error
I think I am not down getting to the 1.0.1 version you mention. I cannot get to the repository with this command: [email protected]:CostaLab/reg-gen.git. I was able to clone through GitHub Desktop and with gh as above, with the same results, downloading version 1.0.0.
Can you indicate how to get to the 1.0.1 version?
Thanks!
Ricardo
from reg-gen.
Hi,
Sorry, the command to download RGT should be:
git clone [email protected]:CostaLab/reg-gen.git
Anyway, since you already downloaded the package through GitHub Desktop, you can switch to develop branch by
git checkout develop
Alternatively, you can try to install rgt via conda, which is what I usually do when running rgt,
- Install miniconda by following https://docs.conda.io/en/latest/miniconda.html
- Once you successfully install conda, create a specific environment for rgt by:
conda create -n rgt python=3.6
- Activate your conda environment:
conda activate rgt
- Install RGT package:
pip install rgt
This will automatically install rgt (v1.0.0) with all its dependencies.
Please let me know if this solves your issue.
from reg-gen.
Hello there,
I successfully installed the develop version 1.0.1 (see attached)
However, I keep getting the same error (see attached)
I am suspecting the issue may be the python version installed by homebrew? In my case this is 3.11. I cannot really think of what else it can be. I will try to install through conda, but before doing so, should I be using an earlier version of Python to install RGT?
from reg-gen.
Hi,
Thanks for the feedback.
I didn't test rgt on python 3.11, for me, python 3.9 works well.
Regarding the error, I think it is because you are running python directly on M1 chip which is an arm64 architecture, and librgt_mac.so was complied for x86_64 through ROSETTA translation.
from reg-gen.
Hi,
Is there a way to compile librgt_mac.so for arm64?
from reg-gen.
Let me give it a try.
from reg-gen.
Sounds good, thanks!
from reg-gen.
Please keep me posted when you have news.
from reg-gen.
Hi,
I installed rgt on my Mac M1 pro, and it worked well.
This means I couldn't reproduce your issue.
Could you provide more information about your python and platform?
You can type python and then:
import platform
platform.uname()
from reg-gen.
Hi Zhijian,
Here the requested information. Hope this helps pinpoint the issue.
from reg-gen.
Hi Zhijian,
I reinstalled cleanly with Python 3.9 but am still getting the same error (see attached). Platform info also attached.
from reg-gen.
Hi,
Thanks for your feedback.
I finally can reproduce your error:
sh hint.sh
**********************************************
Testing HINT
Running HINT using only DNase-seq data..
Downloading test data.
x HINT_DNaseTest/
x HINT_DNaseTest/DNase.bam
x HINT_DNaseTest/DNase.bam.bai
x HINT_DNaseTest/DNasePeaks.bed
Traceback (most recent call last):
File "/opt/homebrew/bin/rgt-hint", line 8, in <module>
sys.exit(main())
^^^^^^
File "/opt/homebrew/lib/python3.11/site-packages/rgt/HINT/Main.py", line 95, in main
args.func(args)
File "/opt/homebrew/lib/python3.11/site-packages/rgt/HINT/Footprinting.py", line 112, in footprinting_run
dnase_seq(args)
File "/opt/homebrew/lib/python3.11/site-packages/rgt/HINT/Footprinting.py", line 529, in dnase_seq
post_processing(footprints=footprints, original_regions=original_regions, fp_min_size=fp_min_size,
File "/opt/homebrew/lib/python3.11/site-packages/rgt/HINT/Footprinting.py", line 812, in post_processing
footprints_overlap = footprints.intersect(original_regions, mode=OverlapType.ORIGINAL)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/opt/homebrew/lib/python3.11/site-packages/rgt/GenomicRegionSet.py", line 732, in intersect
return self.intersect_c(y, mode, rm_duplicates)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/opt/homebrew/lib/python3.11/site-packages/rgt/GenomicRegionSet.py", line 871, in intersect_c
lib = cdll.LoadLibrary(Lib.get_c_rgt())
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/opt/homebrew/Cellar/[email protected]/3.11.4_1/Frameworks/Python.framework/Versions/3.11/lib/python3.11/ctypes/__init__.py", line 454, in LoadLibrary
return self._dlltype(name)
^^^^^^^^^^^^^^^^^^^
File "/opt/homebrew/Cellar/[email protected]/3.11.4_1/Frameworks/Python.framework/Versions/3.11/lib/python3.11/ctypes/__init__.py", line 376, in __init__
self._handle = _dlopen(self._name, mode)
^^^^^^^^^^^^^^^^^^^^^^^^^
OSError: dlopen(/Users/zhijianli/rgtdata/lib/librgt_mac.so, 0x0006): tried: '/Users/zhijianli/rgtdata/lib/librgt_mac.so' (mach-o file, but is an incompatible architecture (have 'x86_64', need 'arm64')), '/System/Volumes/Preboot/Cryptexes/OS/Users/zhijianli/rgtdata/lib/librgt_mac.so' (no such file), '/Users/zhijianli/rgtdata/lib/librgt_mac.so' (mach-o file, but is an incompatible architecture (have 'x86_64', need 'arm64'))
I have modified the code to first check if it's being installed in arm64 or X86_64 platform, and now it works well with Arm64 platform.
To solve it, what you need to do is the following:
-
Delete the rgtdata folder completely, otherise you might still have the x86_64 based library. You can find it in your home directory
-
Pull the new version of RGT to your local machine. Since you already download the repo., you can first switch to develop branch by
git checkout develop
and then pull the code:git pull
. If you think this is too complicated, you can wait until I release it on Pypi, then you just need to install it bypip install rgt
-
After you installed it, please check if you a file called "librgt_mac_arm64.so" in your rgtdata/lib directory:
ls ~/rgtdata/lib
The problem should be solved by following the above steps.
from reg-gen.
Thanks
from reg-gen.
Related Issues (20)
- rgt-hint throwing an error (without any other input) post-installation (Linux) HOT 10
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- OverflowError: cannot convert float infinity to integer HOT 3
- invalid load key, '\x00'
- RGT installation successful, but rgtdata folder is missing. HOT 5
- Question regarding how Lineplots values are calculated, related to #116 HOT 1
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- ResourceWarning: unclosed file (Enable tracemalloc to get the object allocation traceback)
- RGT Hint differential error HOT 5
- Transcription factor scatter plot HOT 2
- aarch64 support
- Result file description
- Fold-change values in THOR differential peaks and post-processed bigwigs
- Extension sizes estimated with THOR HOT 1
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