seqcluster error install

#####command：bin/conda install seqcluster bcbio-nextgen -c bioconda Fetching package metadata: ...... Solving package specifications: . Error: Dependencies missing in current linux-64 channels:

bcbio-nextgen -> ipdb
bcbio-nextgen -> arrow

Did you mean one of these?

idba

You can search for this package on anaconda.org with

anaconda search -t conda arrow

(and similarly for the other packages)

You may need to install the anaconda-client command line client with

conda install anaconda-client

it mean need ipdb，arrow？and i pip install them ，still can't install？ how to solve it？

Nov 13 '17 07:11 wengqi123

Hi,

Normally these errors are temporals, did you try today. In other hands, yes, you can install those packages using pip. Just in case, can you try this:

conda install seqcluster bcbio-nextgen -c bioconda -c conda-forge

Nov 14 '17 18:11 lpantano

when it shows update packages or not，I enter y，but when it Fetching packages，it often can‘t continue feaching packages ，I have tried many times，so I enter n，but when I enter n，it seems nothing install？

Nov 16 '17 00:11 wengqi123

Hi,

sorry about the issues. i am trying to reproduce. Can you paste the whole output of the command I sent you?

For instance this is my output:

root@2639a4aa2851:/# bcbio_conda install seqcluster -c bioconda
Fetching package metadata .............
Solving package specifications: .

Package plan for installation in environment /usr/local/share/bcbio-nextgen/anaconda:

The following packages will be UPDATED:

    conda:      4.3.27-py27_0 conda-forge --> 4.3.30-py27h6ae6dc7_0
    conda-env:  2.6.0-0       conda-forge --> 2.6.0-h36134e3_1
    seqcluster: 1.2.4a-py27_0 bioconda    --> 1.2.4a-py27_2         bioconda

Proceed ([y]/n)? y

conda-env-2.6. 100% |############################################################################################################################################################| Time: 0:00:00   2.15 MB/s
seqcluster-1.2 100% |############################################################################################################################################################| Time: 0:00:00   2.37 MB/s
conda-4.3.30-p 100% |############################################################################################################################################################| Time: 0:00:00  27.46 MB/s
root@2639a4aa2851:/#

As well can you paste here the output of this command?

conda list seqcluster

Mine is this:

root@2639a4aa2851:/# bcbio_conda list seqcluster
# packages in environment at /usr/local/share/bcbio-nextgen/anaconda:
#
seqcluster                1.2.4a                   py27_2    bioconda

Nov 22 '17 14:11 lpantano

command： ./bin/conda install seqcluster bcbio-nextgen -c bioconda -c conda-forge Fetching package metadata: ........ Solving package specifications: ......... Warning: 2 possible package resolutions (only showing differing packages):

statsmodels-0.8.0-py27_0.tar.bz2 statsmodels-0.8.0-np113py27_0.tar.bz2 Package plan for installation in environment /haplox/users/wenger/pipe/RNA/bin/install/seqcluster_v2:

The following packages will be downloaded:

package	build
gettext-0.19.7	1 5.6 MB
icu-58.2	0 22.7 MB
jpeg-9b	2 1.0 MB
krb5-1.14.2	0 4.0 MB
libffi-3.2.1	3 47 KB
libgcc-5.2.0	0 1.1 MB
libgfortran-3.0.0	1 281 KB
libiconv-1.15	0 2.0 MB
libsodium-0.4.5	0 530 KB
libssh2-1.8.0	1 239 KB
mkl-2017.0.3	0 129.5 MB
ncurses-5.9	10 1.1 MB
sqlite-3.13.0	0 4.9 MB
xorg-libxau-1.0.8	3 14 KB
xorg-libxdmcp-1.1.2	3 21 KB
xz-5.2.3	0 854 KB
bedtools-2.26.0	0 739 KB
curl-7.54.1	0 617 KB
dbus-1.10.22	0 1.6 MB
hdf5-1.10.1	0 5.0 MB
libpng-1.6.30	1 220 KB
libxcb-1.12	1 454 KB
libxml2-2.9.5	0 5.0 MB
pcre-8.39	1 656 KB
python-2.7.14	0 13.8 MB
zeromq-4.2.1	1 647 KB
argcomplete-1.8.2	py27_0 40 KB
argh-0.26.2	py27_1 33 KB
asn1crypto-0.22.0	py27_0 146 KB
backports-1.0	py27_1 4 KB
backports_abc-0.5	py27_0 6 KB
bcftools-1.6	0 2.6 MB
beautifulsoup4-4.6.0	py27_0 129 KB
boto-2.48.0	py27_0 1.4 MB
certifi-2017.11.5	py27_0 195 KB
click-6.7	py27_0 101 KB
coverage-4.4.2	py27_0 232 KB
cython-0.27.3	py27_0 7.1 MB
decorator-4.1.2	py27_0 15 KB
dnapi-1.1	py27_2 24 KB
enum34-1.1.6	py27_1 54 KB
fadapa-0.3.1	py27_0 7 KB
freetype-2.7	1 2.8 MB
funcsigs-1.0.2	py_2 13 KB
functools32-3.2.3.2	py27_1 16 KB
futures-3.1.1	py27_0 22 KB
geneimpacts-0.3.3	py27_0 47 KB
glib-2.53.5	0 8.2 MB
htslib-1.6	0 1.1 MB
humanfriendly-4.4	py27_0 82 KB
idna-2.6	py27_1 122 KB
ipaddress-1.0.18	py27_0 31 KB
ipython_genutils-0.1.0	py27_0 33 KB
joblib-0.11	py27_0 190 KB
logbook-1.0.0	py27_0 223 KB
msgpack-python-0.4.8	py27_0 243 KB
netifaces-0.10.6	py27_0 32 KB
numpy-1.13.1	py27_0 6.8 MB
path.py-10.3.1	py27_0 50 KB
progressbar-2.3	py27_0 13 KB
psutil-5.4.0	py27_0 324 KB
ptyprocess-0.5.2	py27_0 21 KB
py-1.5.2	py_0 63 KB
pyasn1-0.3.7	py_0 41 KB
pycparser-2.18	py27_0 167 KB
pyparsing-2.2.0	py27_0 92 KB
pytz-2017.3	py_2 217 KB
pyvcf-0.6.8	py27_0 56 KB
pyzmq-14.7.0	py27_0 669 KB
requests-2.12.4	py27_0 742 KB
ruamel_yaml-0.11.14	py27_1 361 KB
samtools-1.6	0 991 KB
scandir-1.6	py27_0 45 KB
simplegeneric-0.8.1	py27_1 7 KB
simplejson-3.11.1	py27_0 140 KB
sip-4.18	py27_1 265 KB
six-1.11.0	py27_1 20 KB
sqlalchemy-1.1.13	py27_0 1.5 MB
ssl_match_hostname-3.5.0.1	py27_1 8 KB
subprocess32-3.2.7	py27_0 55 KB
tabulate-0.8.1	py_0 23 KB
toolz-0.8.2	py_2 42 KB
wcwidth-0.1.7	py27_0 22 KB
azure-nspkg-1.0.0	py27_0 2 KB
backports.functools_lru_cache-1.4	py27_1 9 KB
backports.shutil_get_terminal_size-1.0.0	py_3 7 KB
biopython-1.70	py27_2 2.5 MB
cffi-1.10.0	py27_0 373 KB
coloredlogs-7.1	py27_0 44 KB
cycler-0.10.0	py27_0 13 KB
fontconfig-2.12.1	6 939 KB
gstreamer-1.8.0	1 3.3 MB
h5py-2.7.1	py27_2 3.4 MB
pathlib2-2.3.0	py27_0 30 KB
pexpect-4.3.0	py27_0 71 KB
pyfaidx-0.5.1	py27_0 40 KB
pygments-2.2.0	py27_0 1.4 MB
pysam-0.13.0	py27_htslib1.6_0 6.8 MB
pytest-3.2.5	py27_0 278 KB
python-dateutil-2.6.1	py27_0 236 KB
requests-toolbelt-0.8.0	py27_0 58 KB
scipy-0.19.1	np113py27_0 35.2 MB
singledispatch-3.4.0.3	py27_0 12 KB
traitlets-4.3.2	py27_0 126 KB
yamllint-1.6.0	py27_0 46 KB
arrow-0.10.0	py_1 30 KB
azure-common-1.1.4	py27_0 4 KB
azure-mgmt-nspkg-1.0.0	py27_0 2 KB
bcrypt-3.1.3	py27_0 59 KB
bioblend-0.10.0	py27_0 156 KB
cryptography-2.0.3	py27_0 859 KB
gffutils-0.9	py27_0 1.2 MB
gst-plugins-base-1.8.0	0 4.0 MB
jupyter_core-4.4.0	py_0 44 KB
pandas-0.21.0	py27_0 24.0 MB
patsy-0.4.1	py27_0 291 KB
pickleshare-0.7.4	py27_0 11 KB
prompt_toolkit-1.0.15	py27_0 332 KB
pynacl-1.1.2	py27_0 552 KB
pytest-cov-2.5.1	py27_0 23 KB
tornado-4.5.2	py27_0 598 KB
azure-mgmt-common-0.20.0	py27_0 8 KB
azure-servicebus-0.20.1	py27_0 43 KB
azure-storage-0.20.3	py27_0 85 KB
ipython-5.5.0	py27_0 1.0 MB
jupyter_client-5.1.0	py27_0 118 KB
paramiko-2.3.1	py_0 119 KB
pbr-3.1.1	py27_0 110 KB
pybedtools-0.7.10	py27_1 12.9 MB
pyopenssl-17.2.0	py27_0 75 KB
qt-5.6.2	3 44.7 MB
statsmodels-0.8.0	py27_0 7.7 MB
azure-mgmt-compute-0.20.1	py27_0 79 KB
azure-mgmt-network-0.20.1	py27_0 91 KB
azure-mgmt-resource-0.20.1	py27_0 42 KB
azure-mgmt-storage-0.20.0	py27_0 24 KB
azure-servicemanagement-legacy-0.20.1	py27_0 97 KB
conda-4.3.30	py27h6ae6dc7_0 507 KB
fabric-1.14.0	py27_0 117 KB
ipykernel-4.6.1	py27_0 140 KB
mock-2.0.0	py27_0 96 KB
pyqt-5.6.0	py27_4 5.1 MB
seqcluster-1.2.4a	py27_2 172 KB
azure-mgmt-0.20.1	py27_0 3 KB
ipyparallel-4.1.0	py27_0 234 KB
matplotlib-2.1.0	py27_1 9.1 MB
pytest-mock-1.6.3	py27_1 14 KB
azure-1.0.3	py27_0 2 KB
ipython-cluster-helper-0.5.9	py27_0 35 KB
seaborn-0.8.1	py27_0 333 KB
cyvcf2-0.8.0	py27_0 2.3 MB
bcbio-nextgen-1.0.7a0	py27_0 924 KB

                                   Total:       413.7 MB

The following NEW packages will be INSTALLED:

argcomplete: 1.8.2-py27_0
argh: 0.26.2-py27_1
arrow: 0.10.0-py_1
asn1crypto: 0.22.0-py27_0
azure: 1.0.3-py27_0
azure-common: 1.1.4-py27_0
azure-mgmt: 0.20.1-py27_0
azure-mgmt-common: 0.20.0-py27_0
azure-mgmt-compute: 0.20.1-py27_0
azure-mgmt-network: 0.20.1-py27_0
azure-mgmt-nspkg: 1.0.0-py27_0
azure-mgmt-resource: 0.20.1-py27_0
azure-mgmt-storage: 0.20.0-py27_0
azure-nspkg: 1.0.0-py27_0
azure-servicebus: 0.20.1-py27_0
azure-servicemanagement-legacy: 0.20.1-py27_0
azure-storage: 0.20.3-py27_0
backports: 1.0-py27_1
backports.functools_lru_cache: 1.4-py27_1
backports.shutil_get_terminal_size: 1.0.0-py_3
backports_abc: 0.5-py27_0
bcbio-nextgen: 1.0.7a0-py27_0
bcftools: 1.6-0
bcrypt: 3.1.3-py27_0
beautifulsoup4: 4.6.0-py27_0
bedtools: 2.26.0-0
bioblend: 0.10.0-py27_0
biopython: 1.70-py27_2
boto: 2.48.0-py27_0
bzip2: 1.0.6-3
certifi: 2017.11.5-py27_0
cffi: 1.10.0-py27_0
click: 6.7-py27_0
coloredlogs: 7.1-py27_0
coverage: 4.4.2-py27_0
cryptography: 2.0.3-py27_0
curl: 7.54.1-0
cycler: 0.10.0-py27_0
cython: 0.27.3-py27_0
cyvcf2: 0.8.0-py27_0
dbus: 1.10.22-0
decorator: 4.1.2-py27_0
dnapi: 1.1-py27_2
enum34: 1.1.6-py27_1
expat: 2.2.1-0
fabric: 1.14.0-py27_0
fadapa: 0.3.1-py27_0
fontconfig: 2.12.1-6
freetype: 2.7-1
funcsigs: 1.0.2-py_2
functools32: 3.2.3.2-py27_1
futures: 3.1.1-py27_0
geneimpacts: 0.3.3-py27_0
gettext: 0.19.7-1
gffutils: 0.9-py27_0
glib: 2.53.5-0
gst-plugins-base: 1.8.0-0
gstreamer: 1.8.0-1
h5py: 2.7.1-py27_2
hdf5: 1.10.1-0
htslib: 1.6-0
humanfriendly: 4.4-py27_0
icu: 58.2-0
idna: 2.6-py27_1
ipaddress: 1.0.18-py27_0
ipykernel: 4.6.1-py27_0
ipyparallel: 4.1.0-py27_0
ipython: 5.5.0-py27_0
ipython-cluster-helper: 0.5.9-py27_0
ipython_genutils: 0.1.0-py27_0
joblib: 0.11-py27_0
jpeg: 9b-2
jupyter_client: 5.1.0-py27_0
jupyter_core: 4.4.0-py_0
krb5: 1.14.2-0
libffi: 3.2.1-3
libgcc: 5.2.0-0
libgfortran: 3.0.0-1
libiconv: 1.15-0
libpng: 1.6.30-1
libsodium: 0.4.5-0
libssh2: 1.8.0-1
libxcb: 1.12-1
libxml2: 2.9.5-0
logbook: 1.0.0-py27_0
matplotlib: 2.1.0-py27_1
mkl: 2017.0.3-0
mock: 2.0.0-py27_0
msgpack-python: 0.4.8-py27_0
ncurses: 5.9-10
netifaces: 0.10.6-py27_0
numpy: 1.13.1-py27_0
pandas: 0.21.0-py27_0
paramiko: 2.3.1-py_0
path.py: 10.3.1-py27_0
pathlib2: 2.3.0-py27_0
patsy: 0.4.1-py27_0
pbr: 3.1.1-py27_0
pcre: 8.39-1
pexpect: 4.3.0-py27_0
pickleshare: 0.7.4-py27_0
progressbar: 2.3-py27_0
prompt_toolkit: 1.0.15-py27_0
psutil: 5.4.0-py27_0
ptyprocess: 0.5.2-py27_0
py: 1.5.2-py_0
pyasn1: 0.3.7-py_0
pybedtools: 0.7.10-py27_1
pycparser: 2.18-py27_0
pyfaidx: 0.5.1-py27_0
pygments: 2.2.0-py27_0
pynacl: 1.1.2-py27_0
pyopenssl: 17.2.0-py27_0
pyparsing: 2.2.0-py27_0
pyqt: 5.6.0-py27_4
pysam: 0.13.0-py27_htslib1.6_0 pytest: 3.2.5-py27_0
pytest-cov: 2.5.1-py27_0
pytest-mock: 1.6.3-py27_1
python-dateutil: 2.6.1-py27_0
pytz: 2017.3-py_2
pyvcf: 0.6.8-py27_0
pyzmq: 14.7.0-py27_0
qt: 5.6.2-3
requests-toolbelt: 0.8.0-py27_0
ruamel_yaml: 0.11.14-py27_1
samtools: 1.6-0
scandir: 1.6-py27_0
scipy: 0.19.1-np113py27_0
seaborn: 0.8.1-py27_0
seqcluster: 1.2.4a-py27_2
simplegeneric: 0.8.1-py27_1
simplejson: 3.11.1-py27_0
singledispatch: 3.4.0.3-py27_0
sip: 4.18-py27_1
six: 1.11.0-py27_1
sqlalchemy: 1.1.13-py27_0
ssl_match_hostname: 3.5.0.1-py27_1
statsmodels: 0.8.0-py27_0
subprocess32: 3.2.7-py27_0
tabulate: 0.8.1-py_0
toolz: 0.8.2-py_2
tornado: 4.5.2-py27_0
traitlets: 4.3.2-py27_0
wcwidth: 0.1.7-py27_0
xorg-libxau: 1.0.8-3
xorg-libxdmcp: 1.1.2-3
xz: 5.2.3-0
yamllint: 1.6.0-py27_0
zeromq: 4.2.1-1
The following packages will be UPDATED:

conda: 4.0.5-py27_0 --> 4.3.30-py27h6ae6dc7_0
conda-env: 2.4.5-py27_0 --> 2.6.0-0
python: 2.7.11-0 --> 2.7.14-0
requests: 2.9.1-py27_0 --> 2.12.4-py27_0
sqlite: 3.9.2-0 --> 3.13.0-0
Proceed ([y]/n)? y

Fetching packages ... Could not connect to https://conda.anaconda.org/conda-forge/linux-64/gettext-0.19.7-1.tar.bz2 Error: Connection error: HTTPSConnectionPool(host='binstar-cio-packages-prod.s3.amazonaws.com', port=443): Max retries exceeded with url: /5718a197878cc672d3c024ab/57199484878cc65fd9694c35?response-content-disposition=attachment%3B%20filename%3D%22gettext-0.19.7-1.tar.bz2%22%3B%20filename%2A%3DUTF-8%27%27gettext-0.19.7-1.tar.bz2&response-content-type=application%2Fx-tar&X-Amz-Algorithm=AWS4-HMAC-SHA256&X-Amz-Expires=60&X-Amz-Date=20171124T030630Z&X-Amz-SignedHeaders=host&X-Amz-Security-Token=FQoDYXdzEDYaDLdTsfpsJW4%2Fge6YZiK3A9%2BxYNXJe4TNXjp%2F0Lcrf9i1o9ms5fVP873CpRXTVqQkZ6Ye6WjZ6bYG5%2Fm90nJqnswrBrknBmU0BhPRCHTtwFLWq%2Boky6EcNRZ8j6TLM1xfvkFU0BIAGiWjrnjAb26PVnAVuSSeLGU0pqDiwYhOXlQ5ApaHmebyGHfFKtJB7qmPHEp45I6E9twO1BBf6WTDqfPQD%2F1CS%2FSRSD62BSqwu8nL67B8mw%2FyM3eQcC%2B6PxS89aYbQxJskuaEieta3zu7X7AyyvQSsewiFK2vWT7uDa%2F51pwEgvGGZn45yQuS5OECCmGlMoNKB1E3xZUg5b1G0fBdNSWqTpp%2BilMCFwsQcOQ14DZHoF6eN5MO7vXZ2A5bsBvXmeeio81kcXyghka9Zlk0uEb8HEKftUVudkilEwhdrR7hsmgHm2Lseo3hkdeVpDQZrWlbKz8nsDI95%2BgUJDumdby%2FCys3ZqZaPWRviappXZMHZm9YL2KRWWM5RDel9NPX9%2BJCWZ0pMP14cxhvBXwneU4Xo5k1vTllbj5M9rkyL5I%2BusT8F7swFIzaIUdWNl6Wf0k9IpVxu0mJhRTg%2FgILoKlFLzsoxfPc0AU%3D&X-Amz-Credential=ASIAJQQTFQH54JDFTOVQ%2F20171124%2Fus-east-1%2Fs3%2Faws4_request&X-Amz-Signature=895641e07ccece1e95ccc9109e98e74bd4e262a1272ef5f5f7d3ebcce921e050 (Caused by NewConnectionError('<requests.packages.urllib3.connection.VerifiedHTTPSConnection object at 0x7fe3c9987c90>: Failed to establish a new connection: [Errno 110] Connection timed out',)): https://conda.anaconda.org/conda-forge/linux-64/gettext-0.19.7-1.tar.bz2

$ ./bin/conda list seqcluster

packages in environment at /pipe/RNA/bin/install/seqcluster_v2:

Nov 24 '17 03:11 wengqi123

Hi,

that seems a connectivity problem.Can you download the package that you get the error:

https://conda.anaconda.org/conda-forge/linux-64/gettext-0.19.7-1.tar.bz2

For me is working. Not sure what is going on. Can I know from where are you connecting? or are you behind a proxy?

Does it gives you always the same error in the same package?

Sorry not to be able to help more.

Nov 27 '17 19:11 lpantano

from China,i can download gettext-0.19.7-1.tar.bz2,maybe some unknown error, i may change other tool,but still thanks for your help.

Dec 02 '17 06:12 wengqi123

Sorry I was unable to help, I am currently preparing a docker instance with everything installed in case that help for you. It will be available tomorrow, I’ll chime in here.

Cheers

On Dec 2, 2017, at 1:17 AM, wengqi123 [email protected] wrote:

from China,i can download gettext-0.19.7-1.tar.bz2,maybe some unknown error, i may change other tool,but still thanks for your help.

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/lpantano/seqcluster/issues/26#issuecomment-348671863, or mute the thread https://github.com/notifications/unsubscribe-auth/ABi_HL9KZSMDjh9cpXk5xZQfJ-7H8lFeks5s8Ot_gaJpZM4QbWLh.

Dec 13 '17 13:12 lpantano

I created a docker image in case you use that: you can install it with docker pull lpantano/smallrna:latest

Cheers

On Dec 13, 2017, at 8:07 AM, Lorena Pantano [email protected] wrote:

Sorry I was unable to help, I am currently preparing a docker instance with everything installed in case that help for you. It will be available tomorrow, I’ll chime in here.

Cheers

On Dec 2, 2017, at 1:17 AM, wengqi123 <[email protected] mailto:[email protected]> wrote:

from China,i can download gettext-0.19.7-1.tar.bz2,maybe some unknown error, i may change other tool,but still thanks for your help.

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/lpantano/seqcluster/issues/26#issuecomment-348671863, or mute the thread https://github.com/notifications/unsubscribe-auth/ABi_HL9KZSMDjh9cpXk5xZQfJ-7H8lFeks5s8Ot_gaJpZM4QbWLh.

Jan 09 '18 20:01 lpantano