Issues running through tutorial

Issue #23 new
Jonathan Greenberg
created an issue

Hello, not very experienced with Unix, python, or github or any of the tools involved here so please bear with me.

I am attempting to run through the MetaPhlAN tutorial and have ran into some difficulty/confusion.

I downloaded gitbash to act as my Unix environment and was able to follow the tutorial fine after getting wget64 as a command in my bin folder.

The part I am on does not seem to process as listed, I can do the first command line $ buccal_mucosa_samples= just fine but the second line doesn't seem to use any commands and just opens up ">" instead of a "$" command line. I tried skipipng down to the wget http download but doing that just initiates endless attempts to connect to downloads.hmpdacc.org which repeatedly get an unknown error.

I made it down to this step: Now, we can download the 20 samples to profile (additional information about the samples is available at the HMP DACC): $ buccal_mucosa_samples="SRS013506 SRS015374 SRS015646 SRS017687 SRS019221 SRS019329 SRS020336 SRS022145 SRS022532 SRS045049" $ for s in ${buccal_mucosa_samples} $ do $ wget http://downloads.hmpdacc.org/data/Illumina/buccal_mucosa/${s}.tar.bz2 -O input/${s}.tar.bz2 $ done $ tongue_dorsum_samples="SRS011243 SRS013234 SRS014888 SRS015941 SRS016086 SRS016342 SRS017713 SRS019219 SRS019327 SRS043663" $ for s in ${tongue_dorsum_samples} $ do $ wget http://downloads.hmpdacc.org/data/Illumina/tongue_dorsum/${s}.tar.bz2 -O input/${s}.tar.bz2 $ done

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