Cellranger 4.0.0 Installation Trouble

Question

[Ethidium Bromide]

Hi all,

I have recently tried installing cellranger-4.0.0 on my server and I ran into an installation failure. This is probably something trivial in my initial step but I thought I would see if anyone can point me in the right direction:

Following directions in Installing Cell Ranger.

I downloaded the tar.gz, the permissions looked okay and then I started with Step 1:

$ tar -xzvf cellranger-4.0.0.tar.gz

Cutting through most of the install and errors it ends with the following:

tar: cellranger-4.0.0/external/anaconda/share/terminfo/a/ansi80x50-mono: Cannot create symlink to `../c/cons50-m': Input/output error
tar: cellranger-4.0.0/external/anaconda/share/terminfo/a/ansi80x50: Cannot create symlink to `../c/cons50': Input/output error
tar: cellranger-4.0.0/external/anaconda/share/terminfo/a/ansi80x43-mono: Cannot create symlink to `../c/cons43-m': Input/output error
tar: cellranger-4.0.0/external/anaconda/share/terminfo/a/ansi80x43: Cannot create symlink to `../c/cons43': Input/output error
tar: cellranger-4.0.0/external/anaconda/share/terminfo/a/ansi80x30-mono: Cannot create symlink to `../c/cons30-m': Input/output error
tar: cellranger-4.0.0/external/anaconda/share/terminfo/a/ansi80x30: Cannot create symlink to `../c/cons30': Input/output error
tar: cellranger-4.0.0/external/anaconda/share/terminfo/a/ansi80x25-raw: Cannot create symlink to `../c/cons25w': Input/output error
tar: cellranger-4.0.0/external/anaconda/share/terminfo/a/ansi80x25-mono: Cannot create symlink to `../c/cons25-m': Input/output error
tar: cellranger-4.0.0/external/anaconda/share/terminfo/a/ansi80x25: Cannot create symlink to `../c/cons25': Input/output error
tar: cellranger-4.0.0/external/anaconda/share/terminfo/a/ansi43m: Cannot create symlink to `../p/pcansi-43-m': Input/output error
tar: cellranger-4.0.0/external/anaconda/share/terminfo/a/addsvp60: Cannot create symlink to `../v/vp60': Input/output error
tar: cellranger-4.0.0/external/anaconda/share/terminfo/a/addsviewpoint: Cannot create symlink to `../v/viewpoint': Input/output error
tar: cellranger-4.0.0/external/anaconda/share/terminfo/X/X-hpterm: Cannot create symlink to `../h/hpterm': Input/output error
tar: cellranger-4.0.0/external/anaconda/share/terminfo/Q/Q310-vip-w-am: Cannot create symlink to `../v/vip-w': Input/output error
tar: cellranger-4.0.0/external/anaconda/share/terminfo/Q/Q310-vip-w: Cannot create symlink to `../v/vip-w': Input/output error
tar: cellranger-4.0.0/external/anaconda/share/terminfo/Q/Q310-vip-Hw: Cannot create symlink to `../v/vip-Hw': Input/output error
tar: cellranger-4.0.0/external/anaconda/share/terminfo/Q/Q310-vip-H-am: Cannot create symlink to `../v/vip-H': Input/output error
tar: cellranger-4.0.0/external/anaconda/share/terminfo/Q/Q310-vip-H: Cannot create symlink to `../v/vip-H': Input/output error
tar: cellranger-4.0.0/external/anaconda/share/terminfo/Q/Q306-8-pc: Cannot create symlink to `../b/bq300-8-pc': Input/output error
tar: cellranger-4.0.0/external/anaconda/share/terminfo/P/P9-W: Cannot create symlink to `../p/prism9-w': Input/output error
tar: cellranger-4.0.0/external/anaconda/share/terminfo/P/P9-8-W: Cannot create symlink to `../p/prism9-8-w': Input/output error
tar: cellranger-4.0.0/external/anaconda/share/terminfo/P/P9-8: Cannot create symlink to `../p/prism9-8': Input/output error
tar: cellranger-4.0.0/external/anaconda/share/terminfo/P/P9: Cannot create symlink to `../p/prism9': Input/output error
tar: cellranger-4.0.0/external/anaconda/share/terminfo/P/P8-W: Cannot create symlink to `../p/prism8-w': Input/output error
tar: cellranger-4.0.0/external/anaconda/share/terminfo/P/P8: Cannot create symlink to `../p/prism8': Input/output error
tar: cellranger-4.0.0/external/anaconda/share/terminfo/P/P7: Cannot create symlink to `../p/prism7': Input/output error
tar: cellranger-4.0.0/external/anaconda/share/terminfo/P/P5: Cannot create symlink to `../p/prism5': Input/output error
tar: cellranger-4.0.0/external/anaconda/share/terminfo/P/P4: Cannot create symlink to `../p/prism4': Input/output error
tar: cellranger-4.0.0/external/anaconda/share/terminfo/P/P14-W: Cannot create symlink to `../p/prism14-w': Input/output error
tar: cellranger-4.0.0/external/anaconda/share/terminfo/P/P14-M-W: Cannot create symlink to `../p/prism14-m-w': Input/output error
tar: cellranger-4.0.0/external/anaconda/share/terminfo/P/P14-M: Cannot create symlink to `../p/prism14-m': Input/output error
tar: cellranger-4.0.0/external/anaconda/share/terminfo/P/P14: Cannot create symlink to `../p/prism14': Input/output error
tar: cellranger-4.0.0/external/anaconda/share/terminfo/P/P12-W: Cannot create symlink to `../p/prism12-w': Input/output error
tar: cellranger-4.0.0/external/anaconda/share/terminfo/P/P12-M-W: Cannot create symlink to `../p/prism12-m-w': Input/output error
tar: cellranger-4.0.0/external/anaconda/share/terminfo/P/P12-M: Cannot create symlink to `../p/prism12-m': Input/output error
tar: cellranger-4.0.0/external/anaconda/share/terminfo/P/P12: Cannot create symlink to `../p/prism12': Input/output error
tar: cellranger-4.0.0/external/anaconda/share/terminfo/N/NCRVT100WPP: Cannot create symlink to `../n/ncrvt100wan': Input/output error
tar: cellranger-4.0.0/external/anaconda/share/terminfo/L/LFT-PC850: Cannot create symlink to `../l/lft': Input/output error
tar: cellranger-4.0.0/external/anaconda/share/terminfo/A/Apple_Terminal: Cannot create symlink to `../n/nsterm': Input/output error
tar: cellranger-4.0.0/external/anaconda/share/terminfo/9/955-w: Cannot create symlink to `../t/tvi955-w': Input/output error
tar: cellranger-4.0.0/external/anaconda/share/terminfo/9/955-hb: Cannot create symlink to `../t/tvi955-hb': Input/output error
tar: cellranger-4.0.0/external/anaconda/share/terminfo/8/8510: Cannot create symlink to `../c/citoh': Input/output error
tar: cellranger-4.0.0/external/anaconda/share/terminfo/7/730MTGr-24: Cannot create symlink to `../a/att730r-24': Input/output error
tar: cellranger-4.0.0/external/anaconda/share/terminfo/7/730MTGr: Cannot create symlink to `../a/att730r': Input/output error
tar: cellranger-4.0.0/external/anaconda/share/terminfo/7/730MTG-41r: Cannot create symlink to `../a/att730r-41': Input/output error
tar: cellranger-4.0.0/external/anaconda/share/terminfo/7/730MTG-41: Cannot create symlink to `../a/att730-41': Input/output error
tar: cellranger-4.0.0/external/anaconda/share/terminfo/7/730MTG-24: Cannot create symlink to `../a/att730-24': Input/output error
tar: cellranger-4.0.0/external/anaconda/share/terminfo/6/630MTG-24: Cannot create symlink to `../a/att630-24': Input/output error
tar: cellranger-4.0.0/external/anaconda/share/terminfo/6/630-lm: Cannot create symlink to `../d/diablo1740-lm': Input/output error
tar: cellranger-4.0.0/external/anaconda/share/terminfo/6/605x-dg: Cannot create symlink to `../d/dg6053': Input/output error
tar: cellranger-4.0.0/external/anaconda/share/terminfo/6/605x: Cannot create symlink to `../d/dg6053': Input/output error
tar: cellranger-4.0.0/external/anaconda/share/terminfo/6/6053-dg: Cannot create symlink to `../d/dg6053': Input/output error
tar: cellranger-4.0.0/external/anaconda/share/terminfo/6/6053: Cannot create symlink to `../d/dg6053': Input/output error
tar: cellranger-4.0.0/external/anaconda/share/terminfo/5/5630DMD-24: Cannot create symlink to `../a/att630-24': Input/output error
tar: cellranger-4.0.0/external/anaconda/share/terminfo/5/5630-24: Cannot create symlink to `../a/att630-24': Input/output error
tar: cellranger-4.0.0/external/anaconda/share/terminfo/5/5620: Cannot create symlink to `../a/att5620': Input/output error
tar: cellranger-4.0.0/external/anaconda/share/terminfo/5/5410-w: Cannot create symlink to `../a/att5410-w': Input/output error
tar: cellranger-4.0.0/external/anaconda/share/terminfo/5/5051: Cannot create symlink to `../i/ibm-pc': Input/output error
tar: cellranger-4.0.0/external/anaconda/share/terminfo/4/4410-w: Cannot create symlink to `../a/att5410-w': Input/output error
tar: cellranger-4.0.0/external/anaconda/share/terminfo/4/4027ex: Cannot create symlink to `../t/tek4025ex': Input/output error
tar: cellranger-4.0.0/external/anaconda/share/terminfo/4/4025ex: Cannot create symlink to `../t/tek4025ex': Input/output error
tar: cellranger-4.0.0/external/anaconda/share/terminfo/3/3b1: Cannot create symlink to `../a/att7300': Input/output error
tar: cellranger-4.0.0/external/anaconda/share/terminfo/3/386at: Cannot create symlink to `../a/att6386': Input/output error
tar: cellranger-4.0.0/external/anaconda/share/terminfo/2/2621a: Cannot create symlink to `../h/hp2621': Input/output error
tar: cellranger-4.0.0/external/anaconda/share/terminfo/2/2621A: Cannot create symlink to `../h/hp2621': Input/output error
tar: cellranger-4.0.0/external/anaconda/share/terminfo/2/2621-wl: Cannot create symlink to `../h/hp2621': Input/output error
tar: cellranger-4.0.0/external/anaconda/share/terminfo/2/2621: Cannot create symlink to `../h/hp2621': Input/output error
tar: cellranger-4.0.0/external/anaconda/share/terminfo/1/1730-lm: Cannot create symlink to `../d/diablo1740-lm': Input/output error
tar: cellranger-4.0.0/external/anaconda/share/terminfo/1/1178: Cannot create symlink to `../a/adm1178': Input/output error
tar: cellranger-4.0.0/external/anaconda/lib/terminfo: Cannot create symlink to `../share/terminfo': Input/output error
tar: Exiting with failure status due to previous errors

...

Looks like Anaconda is where all the problems seem to lay. Not the most experienced in Conda. Anyone have any directions they can point me to in order to fix this?

Thanks for any help in advance!

EtBr

[GenoMax]

Did you try to do this in /opt as the instructions say? You may not have privilege to write there. You should try doing this in a directory that you have write access to.

[newbio17]

If you're on a cluster, it might be time-saving and less stressful to have your administrator install it for you since permission may hinder your efforts like genomax mentioned. There seems to be an older version of Cell Ranger available on conda (courtesy of Holland Computing Center) which should be easier to install. I'm not familiar with Cell Ranger, so you will have to check if there were any significant changes since 3.0.2.

Answer 1

[Ethidium Bromide]

Thank you all. It looks like it was trying to symlink to a variety of dir that I did have the right permissions for for. Sorting this out with my sysadmin.