Can't run this line...

[Gedofs]

Hi! Hope you can help me. I can't run this readme line:

princess all -d ./princess_all -r ont -s reads.split00.fastq.gz reads.split01.fastq.gz -f hs37d5_mainchr.fa

I also tried to run samtools unsuccessfully...

[MeHelmy]

You need to install samtools first. E.g., conda install samtools if you have Conda installed. For more details regarding samtools installation; please, visit http://www.htslib.org/download/

[Gedofs]

thanks @MeHelmy! I installed samtools successfully but now there is a new error besides that, I still can´t this line (princess all -d ./princess_all -r ont -s reads.split00.fastq.gz reads.split01.fastq.gz -f hs37d5_mainchr.fa)

[Gedofs]

Is this step necessary before running a sample or even the test case? where can i download the splitoo fasta?

[MeHelmy]

thanks @MeHelmy! I installed samtools successfully but now there is a new error besides that, I still can´t this line (princess all -d ./princess_all -r ont -s reads.split00.fastq.gz reads.split01.fastq.gz -f hs37d5_mainchr.fa)

As the error explains, it can not find your reference. "Failed to open ....."

[Gedofs]

ok! I fixed that but now im not sure if I need to install this packages as I supposed they were installed during princess

[Gedofs]

Sorry, once again! Still have the same problem. Is it related to conda environment? Hope u can help me

[MeHelmy]

Sorry for the late answer, Which conda version you are using?

[Gedofs]

Thanks for your response. I'm using conda 22.9.0

El lun, 13 feb 2023 a la(s) 17:18, Medhat @.***) escribió:

Sorry for the late answer, Which conda version you are using?

— Reply to this email directly, view it on GitHub https://github.com/MeHelmy/princess/issues/15#issuecomment-1428845337, or unsubscribe https://github.com/notifications/unsubscribe-auth/AWPDKHGASPJ7Q6ICFIFHTCTWXK6LNANCNFSM6AAAAAASAI4IN4 . You are receiving this because you authored the thread.Message ID: @.***>

[MeHelmy]

Hi, we just made an update to reduce Conda dependency. I hope that you can give it a try.

[Gedofs]

Thanks. I'll give a look

El mié, 5 jul 2023 a las 6:32, Medhat @.***>) escribió:

Hi, we just made an update to reduce Conda dependency. I hope that you can give it a try.

— Reply to this email directly, view it on GitHub https://github.com/MeHelmy/princess/issues/15#issuecomment-1621665206, or unsubscribe https://github.com/notifications/unsubscribe-auth/AWPDKHFKAPTVNB6COXKKIVLXOVNF7ANCNFSM6AAAAAASAI4IN4 . You are receiving this because you authored the thread.Message ID: @.***>