Install / locate software on raven / klone

[sr320]

Can you install if needed and list location of these programs on raven and klone?

datasets <- "path"
liftoff  <- "path"
gffread  <- "path"
samtools <- "path"

[kubu4]

Is datasets the NCBI Datasets package?

[sr320]

yes

…

On Tue, Jun 16, 2026 at 9:36 AM kubu4 ***@***.***> wrote: *kubu4* left a comment (RobertsLab/resources#2456) <https://urldefense.com/v3/__https://github.com/RobertsLab/resources/issues/2456*issuecomment-4721071716__;Iw!!K-Hz7m0Vt54!iS8Bc6hTlquJrHrjpz9iiyOrjgdH-Gbpp07UGVV2ajr0mkHCiXrkFynC45sWtFV0Txqmgid5dQcV4Ug81LRoifs$> Is datasets the NCBI Datasets package? — Reply to this email directly, view it on GitHub <https://urldefense.com/v3/__https://github.com/RobertsLab/resources/issues/2456?email_source=notifications&email_token=ABB4PN273CUKYMD3XUWNPEL5AFZPTA5CNFSNUABFM5UWIORPF5TWS5BNNB2WEL2JONZXKZKDN5WW2ZLOOQXTINZSGEYDOMJXGE3KM4TFMFZW63VGMF2XI2DPOKSWK5TFNZ2KYZTPN52GK4S7MNWGSY3L*issuecomment-4721071716__;Iw!!K-Hz7m0Vt54!iS8Bc6hTlquJrHrjpz9iiyOrjgdH-Gbpp07UGVV2ajr0mkHCiXrkFynC45sWtFV0Txqmgid5dQcV4Ug86I0teR0$>, or unsubscribe <https://urldefense.com/v3/__https://github.com/notifications/unsubscribe-auth/ABB4PN47GSGKFVSV652T7BD5AFZPTAVCNFSNUABEKJSXA33TNF2G64TZHM4TSNRZHA3DQOB3JFZXG5LFHM2DMNZVGA3DKMRYHCQXMAQ__;!!K-Hz7m0Vt54!iS8Bc6hTlquJrHrjpz9iiyOrjgdH-Gbpp07UGVV2ajr0mkHCiXrkFynC45sWtFV0Txqmgid5dQcV4Ug893CQvbY$> . You are receiving this because you authored the thread.Message ID: ***@***.***>

[kubu4]

Container has been updated to include liftoff and gffread. The other two programs (datasets and samtools) had already been installed.

All programs are in the system $PATH, so can just be called without a need for a full path.

However, here are the program locations in the container:

datasets <- "/srlab/programs/ncbi-datasets-v13.34.0/datasets"

gffread <- "/srlab/programs/gffread-0.12.9.Linux_x86_64/gffread"

liftoff <- "/srlab/programs/miniforge3-24.7.1-0/envs/liftoff_env/bin/liftoff"

samtools <- "/srlab/programs/samtools-1.20/samtools"

To run the container on Raven, follow the instructions in the Handbook, but use this command to launch this version of the container:

singularity exec \
--bind /tmp:/tmp \
--bind /home:/home \
--bind ~/rstudio-server/var-lib:/var/lib/rstudio-server \
--bind ~/rstudio-server/var-run:/var/run/rstudio-server \
--bind ~/rstudio-server/tmp:/tmp/rstudio-server \
/gscratch/srlab/containers/srlab-R4.4-bioinformatics-container-d606e0f.sif \
rserver --www-port 8788 --www-address 0.0.0.0 --server-user=$(whoami)

Currently, Klone is offline for maintenance, so can't get the container on there just yet. When it comes back online, I'll add it.

[sr320]

if in path would this not work?

(.venv) (base) sr320@raven:/home/shared/16TB_HDD_01/sr320/github/project-lake-trout$ datasets
datasets: command not found

[kubu4]

if in path would this not work?

No, because it's installed in the bioinformatics container on Raven.

Want me to also install these directly on Raven as well?

[sr320]

Yes please

…

On Wed, Jun 17, 2026 at 12:41 PM kubu4 ***@***.***> wrote: *kubu4* left a comment (RobertsLab/resources#2456) <https://urldefense.com/v3/__https://github.com/RobertsLab/resources/issues/2456*issuecomment-4734516499__;Iw!!K-Hz7m0Vt54!mFxyiw2Rm2uBUACdGSUe5zoO2MkwLDR4-j9-Fj6spa1mJbviu9fgLRFJdmqNhnZhF93c3ikz8zJufmJgR4SqoOI$> if in path would this not work? No, because it's installed in the bioinformatics container on Raven. Want me to also install these directly on Raven as well? — Reply to this email directly, view it on GitHub <https://urldefense.com/v3/__https://github.com/RobertsLab/resources/issues/2456?email_source=notifications&email_token=ABB4PN4JDT2ATSWWIPDHDQL5ALX5NA5CNFSNUABFM5UWIORPF5TWS5BNNB2WEL2JONZXKZKDN5WW2ZLOOQXTINZTGQ2TCNRUHE42M4TFMFZW63VGMF2XI2DPOKSWK5TFNZ2KYZTPN52GK4S7MNWGSY3L*issuecomment-4734516499__;Iw!!K-Hz7m0Vt54!mFxyiw2Rm2uBUACdGSUe5zoO2MkwLDR4-j9-Fj6spa1mJbviu9fgLRFJdmqNhnZhF93c3ikz8zJufmJgngmxx6Q$>, or unsubscribe <https://urldefense.com/v3/__https://github.com/notifications/unsubscribe-auth/ABB4PNZ4PX2YMLQUX2V4BCD5ALX5NAVCNFSNUABEKJSXA33TNF2G64TZHM4TSNRZHA3DQOB3JFZXG5LFHM2DMNZVGA3DKMRYHCQXMAQ__;!!K-Hz7m0Vt54!mFxyiw2Rm2uBUACdGSUe5zoO2MkwLDR4-j9-Fj6spa1mJbviu9fgLRFJdmqNhnZhF93c3ikz8zJufmJg-7DP1qA$> . You are receiving this because you authored the thread.Message ID: ***@***.***>

[kubu4]

Raven system locations:

datasets <- "/home/shared/ncbi-datasets-v13.34.0datasets"

gffread <- "/home/shared/gffread-0.12.7.Linux_x86_64/gffread"

liftoff <- "/opt/anaconda/anaconda3/envs/liftoff_env/bin/liftoff"

samtools <- "/home/shared/samtools-1.12/samtools"

NOTE: None of these are in the system $PATH, so will require full path to use.

[kubu4]

Container is now on Klone:

/gscratch/srlab/containers/srlab-R4.4-bioinformatics-container-46b5d9e.sif