conda create -n leafcutter python=2.7
conda activate leafcutter
samtools
regtools
conda install -c bioconda regtools
regtools install
清华镜像源怀疑有问题，所以重新加了豆瓣的镜像源，但是安装包还是不行
先删除所有的镜像
conda config --remove-key channels
添加镜像
conda config --add channels https://pypi.douban.com/anaconda/cloud/conda-forge/
conda config --add channels https://pypi.douban.com/anaconda/cloud/msys2/
conda config --add channels https://pypi.douban.com/anaconda/cloud/bioconda/
conda config --add channels https://pypi.douban.com/anaconda/cloud/menpo/
conda config --add channels https://pypi.douban.com/anaconda/cloud/pytorch/
显示源
conda config --set show_channel_urls yes
显示目前的镜像
conda config --show-sources
查看
(leafcutter)... data1/jiarongf/specise_compare_HGPS/AS
$
history conda config --set ssl_verify TRUE
-bash: history: conda: numeric argument required
(leafcutter) .../data1/jiarongf/specise_compare_HGPS/AS
$
conda config --set ssl_verify TRUE
(leafcutter) .../data1/jiarongf/specise_compare_HGPS/AS
$
conda config --show-sources
==> /home/jiarongf/.condarc <==
envs_dirs:
- /data1/jiarongf/anaconda3/envs
- ~/my-envs
ssl_verify: True
channels:
- https://pypi.douban.com/anaconda/cloud/bioconda/
- https://pypi.douban.com/anaconda/cloud/pytorch/
- https://pypi.douban.com/anaconda/cloud/menpo/
- https://pypi.douban.com/anaconda/cloud/msys2/
- https://pypi.douban.com/anaconda/cloud/conda-forge/
- defaults
show_channel_urls: True
还是没有安装成功，
报错原因
Collecting package metadata (current_repodata.json): ...working... failed
# >>>>>>>>>>>>>>>>>>>>>> ERROR REPORT <<<<<<<<<<<<<<<<<<<<<<
Traceback (most recent call last):
File "/data1/jiarongf/anaconda_se/anaconda3/lib/python3.8/site-packages/conda/exceptions.py", line 1125, in __call__
return func(*args, **kwargs)
File "/data1/jiarongf/anaconda_se/anaconda3/lib/python3.8/site-packages/conda/cli/main.py", line 86, in main_subshell
exit_code = do_call(args, p)
File "/data1/jiarongf/anaconda_se/anaconda3/lib/python3.8/site-packages/conda/cli/conda_argparse.py", line 93, in do_call
return getattr(module, func_name)(args, parser)
File "/data1/jiarongf/anaconda_se/anaconda3/lib/python3.8/site-packages/conda/notices/core.py", line 72, in wrapper
return_value = func(*args, **kwargs)
File "/data1/jiarongf/anaconda_se/anaconda3/lib/python3.8/site-packages/conda/cli/main_install.py", line 22, in execute
install(args, parser, 'install')
File "/data1/jiarongf/anaconda_se/anaconda3/lib/python3.8/site-packages/conda/cli/install.py", line 256, in install
unlink_link_transaction = solver.solve_for_transaction(
File "/data1/jiarongf/anaconda_se/anaconda3/lib/python3.8/site-packages/conda/core/solve.py", line 152, in solve_for_transaction
unlink_precs, link_precs = self.solve_for_diff(update_modifier, deps_modifier,
File "/data1/jiarongf/anaconda_se/anaconda3/lib/python3.8/site-packages/conda/core/solve.py", line 195, in solve_for_diff
final_precs = self.solve_final_state(update_modifier, deps_modifier, prune, ignore_pinned,
File "/data1/jiarongf/anaconda_se/anaconda3/lib/python3.8/site-packages/conda/core/solve.py", line 300, in solve_final_state
ssc = self._collect_all_metadata(ssc)
File "/data1/jiarongf/anaconda_se/anaconda3/lib/python3.8/site-packages/conda/common/io.py", line 86, in decorated
return f(*args, **kwds)
File "/data1/jiarongf/anaconda_se/anaconda3/lib/python3.8/site-packages/conda/core/solve.py", line 463, in _collect_all_metadata
index, r = self._prepare(prepared_specs)
File "/data1/jiarongf/anaconda_se/anaconda3/lib/python3.8/site-packages/conda/core/solve.py", line 1057, in _prepare
reduced_index = get_reduced_index(self.prefix, self.channels,
File "/data1/jiarongf/anaconda_se/anaconda3/lib/python3.8/site-packages/conda/core/index.py", line 297, in get_reduced_index
new_records = SubdirData.query_all(spec, channels=channels, subdirs=subdirs,
File "/data1/jiarongf/anaconda_se/anaconda3/lib/python3.8/site-packages/conda/core/subdir_data.py", line 152, in query_all
result = tuple(concat(executor.map(subdir_query, channel_urls)))
File "/data1/jiarongf/anaconda_se/anaconda3/lib/python3.8/concurrent/futures/_base.py", line 611, in result_iterator
yield fs.pop().result()
File "/data1/jiarongf/anaconda_se/anaconda3/lib/python3.8/concurrent/futures/_base.py", line 439, in result
return self.__get_result()
File "/data1/jiarongf/anaconda_se/anaconda3/lib/python3.8/concurrent/futures/_base.py", line 388, in __get_result
raise self._exception
File "/data1/jiarongf/anaconda_se/anaconda3/lib/python3.8/concurrent/futures/thread.py", line 57, in run
result = self.fn(*self.args, **self.kwargs)
File "/data1/jiarongf/anaconda_se/anaconda3/lib/python3.8/site-packages/conda/core/subdir_data.py", line 144, in
subdir_query = lambda url: tuple(SubdirData(Channel(url), repodata_fn=repodata_fn).query(
File "/data1/jiarongf/anaconda_se/anaconda3/lib/python3.8/site-packages/conda/core/subdir_data.py", line 157, in query
self.load()
File "/data1/jiarongf/anaconda_se/anaconda3/lib/python3.8/site-packages/conda/core/subdir_data.py", line 222, in load
_internal_state = self._load()
File "/data1/jiarongf/anaconda_se/anaconda3/lib/python3.8/site-packages/conda/core/subdir_data.py", line 419, in _load
_internal_state = self._process_raw_repodata_str(raw_repodata_str)
File "/data1/jiarongf/anaconda_se/anaconda3/lib/python3.8/site-packages/conda/core/subdir_data.py", line 492, in _process_raw_repodata_str
json_obj = json.loads(raw_repodata_str or '{}')
File "/data1/jiarongf/anaconda_se/anaconda3/lib/python3.8/json/__init__.py", line 357, in loads
return _default_decoder.decode(s)
File "/data1/jiarongf/anaconda_se/anaconda3/lib/python3.8/json/decoder.py", line 337, in decode
obj, end = self.raw_decode(s, idx=_w(s, 0).end())
File "/data1/jiarongf/anaconda_se/anaconda3/lib/python3.8/json/decoder.py", line 353, in raw_decode
obj, end = self.scan_once(s, idx)
json.decoder.JSONDecodeError: Expecting property name enclosed in double quotes: line 1 column 98 (char 97)
`$ /data1/jiarongf/anaconda_se/anaconda3/bin/conda install -c bioconda regtools`
environment variables:
CIO_TEST=
CONDA_DEFAULT_ENV=leafcutter
CONDA_EXE=/data1/jiarongf/anaconda_se/anaconda3/bin/conda
CONDA_PREFIX=/data1/jiarongf/anaconda3/envs/leafcutter
CONDA_PREFIX_1=/data1/jiarongf/anaconda_se/anaconda3
CONDA_PROMPT_MODIFIER=(leafcutter)
CONDA_PYTHON_EXE=/data1/jiarongf/anaconda_se/anaconda3/bin/python
CONDA_ROOT=/data1/jiarongf/anaconda_se/anaconda3
CONDA_SHLVL=2
CURL_CA_BUNDLE=
MANPATH=/data1/jiarongf/learning/cancer-
WES/run/gnuplot-5.4.3/gnuplot/share/man/man1:
PATH=/data1/jiarongf/anaconda_se/anaconda3/bin:/home/jiarongf/.local/bin:/d
ata1/jiarongf/software/TrimGalore-0.6.6:/data1/jiarongf/HGPS_Hic_seq/h
ic-pro/HiC-Pro-3.1.0/bin:/home/jiarongf/.aspera/connect/bin:/data1/jia
rongf/anaconda3/envs/KG/lib/nltk_data-gh-
pages/nltk_data:/data1/jiarongf/learning/cancer-WES/run/gatk-4.2.6.1:/
data1/jiarongf/other:/data1/jiarongf/learning/cancer-
WES/run/gnuplot-5.4.3/gnuplot/bin:/data1/jiarongf/learning/cancer-WES/
run:/data1/tongxin/software/annovar:/data1/jiarongf/anaconda_se/anacon
da3/bin/python:/data1/jiarongf/software:/data1/jiarongf/software/ncbi-
blast/bin:/data1/jiarongf/software/sratoolkit.2.11.0-centos_linux64/bi
n:/data1/nyy/HGPS_scRNAseq/cellranger-6.0.1:/data1/jiarongf/RNA_seq/tr
anscript/data/RNAseq/RNAseq/subread-1.6.0-Linux-x86_64/bin:/data1/jiar
ongf/RNA_seq/transcript/fastp:/data1/jiarongf/Knowledge_Graph/metamap/
metamap_bag/bag/public_mm/bin:/data1/jiarongf/software/jdl/jdk-11.0.10
/bin:/home/jiarongf/.conda/envs/jupyter_notebook/lib/python3.6/site-pa
ckages:/data1/neo4j/neo4j-community-4.2.1/bin:/data/yangpp/Space_Range
r/spaceranger-1.2.0:/data1/jiarongf/anaconda3/envs/leafcutter/bin:/dat
a1/jiarongf/anaconda_se/anaconda3:/data1/jiarongf/anaconda_se/anaconda
3/bin:/data1/jiarongf/anaconda_se/anaconda3/condabin:/data/anaconda3/b
in:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/g
ames:/usr/local/games:/snap/bin
PKG_CONFIG_PATH=/data1/jiarongf/anaconda3/lib/pkgconfig
REF_PATH=$/data1/jiarongf/learning/cancer-
WES/5.GATK/ref/cache/%2s/%2s/%s:http://www.ebi.ac.uk/ena/cram/md5/%s
REQUESTS_CA_BUNDLE=
SSL_CERT_FILE=
active environment : leafcutter
active env location : /data1/jiarongf/anaconda3/envs/leafcutter
shell level : 2
user config file : /home/jiarongf/.condarc
populated config files : /home/jiarongf/.condarc
conda version : 4.14.0
conda-build version : 3.21.4
python version : 3.8.8.final.0
virtual packages : __linux=5.4.0=0
__glibc=2.27=0
__unix=0=0
__archspec=1=x86_64
base environment : /data1/jiarongf/anaconda_se/anaconda3 (writable)
conda av data dir : /data1/jiarongf/anaconda_se/anaconda3/etc/conda
conda av metadata url : None
channel URLs : https://conda.anaconda.org/bioconda/linux-64
https://conda.anaconda.org/bioconda/noarch
http://mirrors.ustc.edu.cn/anaconda/pkgs/free/linux-64
http://mirrors.ustc.edu.cn/anaconda/pkgs/free/noarch
http://pypi.douban.com/anaconda/cloud/bioconda/linux-64
http://pypi.douban.com/anaconda/cloud/bioconda/noarch
http://pypi.douban.com/anaconda/cloud/pytorch/linux-64
http://pypi.douban.com/anaconda/cloud/pytorch/noarch
http://pypi.douban.com/anaconda/cloud/menpo/linux-64
http://pypi.douban.com/anaconda/cloud/menpo/noarch
http://pypi.douban.com/anaconda/cloud/msys2/linux-64
http://pypi.douban.com/anaconda/cloud/msys2/noarch
http://pypi.douban.com/anaconda/cloud/conda-forge/linux-64
http://pypi.douban.com/anaconda/cloud/conda-forge/noarch
package cache : /data1/jiarongf/anaconda_se/anaconda3/pkgs
/home/jiarongf/.conda/pkgs
envs directories : /data1/jiarongf/anaconda3/envs
/home/jiarongf/my-envs
/data1/jiarongf/anaconda_se/anaconda3/envs
/home/jiarongf/.conda/envs
platform : linux-64
user-agent : conda/4.14.0 requests/2.25.1 CPython/3.8.8 Linux/5.4.0-110-generic ubuntu/18.04.6 glibc/2.27
UID:GID : 1005:1005
netrc file : None
offline mode : False
An unexpected error has occurred. Conda has prepared the above report.
If submitted, this report will be used by core maintainers to improve
future releases of conda.
Would you like conda to send this report to the core maintainers?
[y/N]:
Timeout reached. No report sent.
没有解决，
用gitclone安装