Install erro

[huangyuanf]

I have installed minimap2 by conda,but when I run python setup.py install ,I got such information: Traceback (most recent call last): File "setup.py", line 57, in if not check_minimap2(): sys.exit('Dependency problem: minimap2 >= 2.0 not found') File "setup.py", line 8, in check_minimap2 p = subprocess.Popen(['minimap2', '--version'], stdout=subprocess.PIPE) File "/lustre/huangyf/software/Miniconda3/lib/python3.8/subprocess.py", line 854, in init self._execute_child(args, executable, preexec_fn, close_fds, File "/lustre/huangyf/software/Miniconda3/lib/python3.8/subprocess.py", line 1702, in _execute_child raise child_exception_type(errno_num, err_msg, err_filename) FileNotFoundError: [Errno 2] No such file or directory: 'minimap2'

please help me

[adamewing]

Can you run minimap2 by itself outside of tldr?

[huangyuanf]

 thanks! Yes,I can run minimap2,but I can not install TLDR,my python version is Python 3.8.5,so I don know why. 

------------------ 原始邮件 ------------------ 发件人: "adamewing/tldr" @.>; 发送时间: 2021年7月13日(星期二) 晚上9:30 @.>; @.**@.>; 主题: Re: [adamewing/tldr] Install erro (#16)

Can you run minimap2 by itself outside of tldr?

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[huangyuanf]

I have resolved the question.But when I run /lustre/huangyf/software/tldr-1.2.2/tldr/tldr" --help ;I got information as following: Traceback (most recent call last): File "/lustre/huangyf/software/tldr-1.2.2/tldr/tldr", line 17, in from bx.intervals.intersection import Intersecter, Interval ImportError: No module named bx.intervals.intersection

I try to conda install bx.intervals.intersection -y but failed,so how to resolve it .Thanks!

[adamewing]

The package name for that one is bx-python so try either conda install -c bioconda bx-python or pip install bx-python. Hope that helps.

[huangyuanf]

First step ,I use conda installing minimap=2.21-r1071,exonerate=2.4.0,samtools=1.8,MAFFT v7.480, the path of all is /lustre/huangyf/software/Miniconda3/bin/ ;then I downloaded the tldr-1.2.2 .tar.gz from this page , then I use tar -zxvf tldr-1.2.2 .tar.gz and change directory to tldr-1.2.2 but when I run python setup.py install,I got such information: Traceback (most recent call last): File "setup.py", line 57, in if not check_minimap2(): sys.exit('Dependency problem: minimap2 >= 2.0 not found') File "setup.py", line 8, in check_minimap2 p = subprocess.Popen(['minimap2', '--version'], stdout=subprocess.PIPE) File "/lustre/huangyf/software/Miniconda3/lib/python3.8/subprocess.py", line 854, in init self._execute_child(args, executable, preexec_fn, close_fds, File "/lustre/huangyf/software/Miniconda3/lib/python3.8/subprocess.py", line 1702, in _execute_child raise child_exception_type(errno_num, err_msg, err_filename) FileNotFoundError: [Errno 2] No such file or directory: 'minimap2'

then I found if I copy minimap=22.21-r1071,exonerate=2.4.0,samtools=1.8,MAFFT v7.480 to tldr directory,I can install it ,but when I run I run tldr,I got such information: Traceback (most recent call last): File "/lustre/huangyf/software/Miniconda3/lib/python3.8/multiprocessing/pool.py", line 125, in worker result = (True, func(*args, **kwds)) File "/lustre/huangyf/software/tldr/build/scripts-3.8/tldr", line 1270, in process_cluster te = te_align(te_lib, insread.r_seq_trimmed) File "/lustre/huangyf/software/tldr/build/scripts-3.8/tldr", line 851, in te_align p = subprocess.Popen(cmd, stdout=subprocess.PIPE, stderr=subprocess.PIPE) File "/lustre/huangyf/software/Miniconda3/lib/python3.8/subprocess.py", line 854, in init self._execute_child(args, executable, preexec_fn, close_fds, File "/lustre/huangyf/software/Miniconda3/lib/python3.8/subprocess.py", line 1702, in _execute_child raise child_exception_type(errno_num, err_msg, err_filename) FileNotFoundError: [Errno 2] No such file or directory: 'exonerate' """

The above exception was the direct cause of the following exception:

Traceback (most recent call last): File "/lustre/huangyf/software/tldr/build/scripts-3.8/tldr", line 2083, in main(args) File "/lustre/huangyf/software/tldr/build/scripts-3.8/tldr", line 1873, in main processed_clusters.append(res.get()) File "/lustre/huangyf/software/Miniconda3/lib/python3.8/multiprocessing/pool.py", line 771, in get raise self._value FileNotFoundError: [Errno 2] No such file or directory: 'exonerate'

so,I don't known what's wrong? Thanks for your help

[adamewing]

Are you able to run the commands for those tools (minimap2, exonerate, mafft) outside of tldr? If so, are you sure you're running tldr in the same environment and/or same machine as the dependencies?

[huangyuanf]

en,how can I make sure running tldr in the same environment and/or same machine as the dependencies? I don't understand this,what should I do?