SEA-PHAGES | New File Checker for Mac

Link to this post \| posted 25 Jun, 2021 20:26
kbutela	Does anyone have instructions for installing the new flat file checker on MacOS? I'm trying from the pdm_utils page but keep hitting a lot of roadblocks with things not working as described.

Link to this post \| posted 26 Jun, 2021 16:43
chg60	Hi Kristen, Sorry the ReadTheDocs instructions don't seem to be working for you. I'll spend some time reviewing those and hopefully get it straightened out. Would be helpful to hear from you if there are steps in particular not working. In the meantime, would you mind trying to use the instructions and resources found in the attached .zip file? Instructions are still a work in progress so if anything still needs to be clarified please let me know! Best, Christian 22Kb

Link to this post | posted 26 Jun, 2021 16:43

chg60

Hi Kristen,

Sorry the ReadTheDocs instructions don't seem to be working for you. I'll spend some time reviewing those and hopefully get it straightened out. Would be helpful to hear from you if there are steps in particular not working.

In the meantime, would you mind trying to use the instructions and resources found in the attached .zip file? Instructions are still a work in progress so if anything still needs to be clarified please let me know!

Best,

Christian

Link to this post \| posted 28 Jun, 2021 14:21
kbutela	Hi Christian- Thanks for this new set of instructions! Unfortunately I still get stuck fairly early in the process. When I update my bash_profile file with `nano ~/.bash_profile export $PATH=’$PATH:/usr/local/mysql/bin’` I get this error message: `/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/opt/X11/bin=$PATH:/usr/local/mysql/bin': not a valid identifier` I am unsure how to proceed. I can try to create a new bash_profile file but other than this I'm out of ideas. UPDATE: I looked on some help forums and they suggested changing `export $PATH=’$PATH:/usr/local/mysql/bin’` to `export PATH=’$PATH:/usr/local/mysql/bin’` This seems to have solved the problem and I am proceeding with the install. I am going to edit a version of the instructions as I go. Edited 28 Jun, 2021 14:36

Link to this post | posted 28 Jun, 2021 14:21

kbutela

Hi Christian-

Thanks for this new set of instructions! Unfortunately I still get stuck fairly early in the process. When I update my bash_profile file with

nano ~/.bash_profile
export $PATH=’$PATH:/usr/local/mysql/bin’

I get this error message:

/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/opt/X11/bin=$PATH:/usr/local/mysql/bin': not a valid identifier

I am unsure how to proceed. I can try to create a new bash_profile file but other than this I'm out of ideas.

UPDATE: I looked on some help forums and they suggested changing

export $PATH=’$PATH:/usr/local/mysql/bin’

export PATH=’$PATH:/usr/local/mysql/bin’

This seems to have solved the problem and I am proceeding with the install. I am going to edit a version of the instructions as I go.

Edited 28 Jun, 2021 14:36

Link to this post \| posted 28 Jun, 2021 14:33
chg60	Ugh - Sorry Kristen, Claire Rinehart pointed that one out to me already and I forgot to update the document to reflect that. I'd be grateful for your annotated version when you're done.

Link to this post \| posted 28 Jun, 2021 16:45
kbutela	Thanks Christian! I have the file checker running on my Mac now and I was able to successfully run it with a test genome. I have attached the original instructions file with my edits and screenshots. I encountered a few more hiccups but I was able to solve them, so I put in my workarounds and triggered error messages in the document on the steps where the problems occurred. 250Kb

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