Please Help! Installation Error from Conda

Question

Please Help! Installation Error from Conda

jsolvason opened this issue 6 years ago · comments

I am installing on Ubuntu 16.04.4 LTS
Anaconda = 5.1

$ conda install -c bioconda bpipe
Solving environment: failed

PackagesNotFoundError: The following packages are not available from current channels:

  - bpipe
  - openjdk=8.0[build=zulu8*]

Current channels:

  - https://conda.anaconda.org/bioconda/linux-64
  - https://conda.anaconda.org/bioconda/noarch
  - https://repo.continuum.io/pkgs/main/linux-64
  - https://repo.continuum.io/pkgs/main/noarch
  - https://repo.continuum.io/pkgs/free/linux-64
  - https://repo.continuum.io/pkgs/free/noarch
  - https://repo.continuum.io/pkgs/r/linux-64
  - https://repo.continuum.io/pkgs/r/noarch
  - https://repo.continuum.io/pkgs/pro/linux-64
  - https://repo.continuum.io/pkgs/pro/noarch

I tried Installing the packages separately by simply downloading the tar files and it seemed to work, although I kept getting grep: warning: GREP_OPTIONS is deprecated; please use an alias or script errors. Bowtie takes much longer than expected.

Thoughts?

$ bpipe
grep: warning: GREP_OPTIONS is deprecated; please use an alias or script
grep: warning: GREP_OPTIONS is deprecated; please use an alias or script
grep: warning: GREP_OPTIONS is deprecated; please use an alias or script
grep: warning: GREP_OPTIONS is deprecated; please use an alias or script
grep: warning: GREP_OPTIONS is deprecated; please use an alias or script
grep: warning: GREP_OPTIONS is deprecated; please use an alias or script

Bpipe Version 0.9.9.2   Built on Mon Jul 18 03:11:39 UTC 2016

$ bpipe run ../parclip-pipe-chimeraAdapters.sh Pilot2-PAR-Clip_S1_L001_R1_001.fastq 
grep: warning: GREP_OPTIONS is deprecated; please use an alias or script
grep: warning: GREP_OPTIONS is deprecated; please use an alias or script
grep: warning: GREP_OPTIONS is deprecated; please use an alias or script
grep: warning: GREP_OPTIONS is deprecated; please use an alias or script
grep: warning: GREP_OPTIONS is deprecated; please use an alias or script
grep: warning: GREP_OPTIONS is deprecated; please use an alias or script
====================================================================================================
|                              Starting Pipeline at 2018-04-04 18:59                               |
====================================================================================================

========================================= Stage preprocess =========================================

Simon Sadedin · Answer 1 · Thu Apr 05 2018 04:54:18 GMT+0800 (China Standard Time)

Hi, Unfortunately I haven't made a conda installer for bpipe yet - it's not an area I'm super knowledgable about. If someone contributes it then it would be very nice to have. The GREP_OPTIONS error seems like it could be coming from your environment - do you have that environment variable set? try doing this: unset GREP_OPTIONS before running bpipe. If that works for you then I'll added it to the bpipe launcher script so that others don't hit this problem. Cheers, Simon

…

On Thu, Apr 5, 2018 at 5:41 AM, jsolvason ***@***.***> wrote: I am installing on Ubuntu 16.04.4 LTS Anaconda = 5.1 $ conda install -c bioconda bpipe Solving environment: failed PackagesNotFoundError: The following packages are not available from current channels: - bpipe - openjdk=8.0[build=zulu8*] Current channels: - https://conda.anaconda.org/bioconda/linux-64 - https://conda.anaconda.org/bioconda/noarch - https://repo.continuum.io/pkgs/main/linux-64 - https://repo.continuum.io/pkgs/main/noarch - https://repo.continuum.io/pkgs/free/linux-64 - https://repo.continuum.io/pkgs/free/noarch - https://repo.continuum.io/pkgs/r/linux-64 - https://repo.continuum.io/pkgs/r/noarch - https://repo.continuum.io/pkgs/pro/linux-64 - https://repo.continuum.io/pkgs/pro/noarch I tried Installing the packages separately by simply downloading the tar files and it seemed to work, although I kept getting grep: warning: GREP_OPTIONS is deprecated; please use an alias or script errors. Bowtie takes much longer than expected. Thoughts? $ bpipe grep: warning: GREP_OPTIONS is deprecated; please use an alias or script grep: warning: GREP_OPTIONS is deprecated; please use an alias or script grep: warning: GREP_OPTIONS is deprecated; please use an alias or script grep: warning: GREP_OPTIONS is deprecated; please use an alias or script grep: warning: GREP_OPTIONS is deprecated; please use an alias or script grep: warning: GREP_OPTIONS is deprecated; please use an alias or script Bpipe Version 0.9.9.2 Built on Mon Jul 18 03:11:39 UTC 2016 $ bpipe run ../parclip-pipe-chimeraAdapters.sh Pilot2-PAR-Clip_S1_L001_R1_001.fastq grep: warning: GREP_OPTIONS is deprecated; please use an alias or script grep: warning: GREP_OPTIONS is deprecated; please use an alias or script grep: warning: GREP_OPTIONS is deprecated; please use an alias or script grep: warning: GREP_OPTIONS is deprecated; please use an alias or script grep: warning: GREP_OPTIONS is deprecated; please use an alias or script grep: warning: GREP_OPTIONS is deprecated; please use an alias or script ==================================================================================================== | Starting Pipeline at 2018-04-04 18:59 | ==================================================================================================== ========================================= Stage preprocess ========================================= — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#233>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AAIedEdgWywBWnKe3fdQ8_Om6xcPHg60ks5tlSIAgaJpZM4THYhn> .

Joe Solvason · Answer 2 · Fri Apr 06 2018 01:51:16 GMT+0800 (China Standard Time)

Ah I see. I copied some lines to the .bashrc from an old copy from another server. That seemed to correct the issue. Thanks!

Joe