Missing input files for rule symlinks

[EugeneEA]

Hi, I'm trying to launch run of spacemake I've installed everything and bump into two errors:

first. spacemake init --dropseq_tools /home/eugenea/bin/Drop-seq_tools-2.5.1 --download_species human --download_species finishes snakemake part, but seems to fails later

Second. (after re-init with the downloaded genomes spacemake config add_species --name homo_sapiens --reference genome --sequence /home/eugenea/spacemake_test/species_data/human/human_genome.fa --annotation /home/eugenea/spacemake_test/species_data/human/human_annotation.gtf ) Spacemake fails to build dag

project was added like in the docs:

spacemake projects add_sample \
   --project_id spacemake_test_run \
   --sample_id visq_test \
   --R1 /home/data/fastq/100086/scRNAseq/vis1_S1_L001_R1_001.fastq.gz /home/data/fastq/100086/scRNAseq/vis1_S1_L002_R1_001.fastq.gz \
   --R2 /home/data/fastq/100086/scRNAseq/vis1_S1_L001_R2_001.fastq.gz /home/data/fastq/100086/scRNAseq/vis1_S1_L002_R2_001.fastq.gz \
   --species homo_sapiens \
   --puck visium \
   --run_mode visium \
   --barcode_flavor visium

Best, Eugene

[sztankatt]

Hi @EugeneEA,

Thank you for using spacemake! Can you confirm that your spacemake version is 0.7?

I think something got broken when upgrading from 0.5.5 to 0.7.

I would suggest you install the former with pip install spacemake==0.5.5 and try these commands again.

Let me know if it works.

Best, Tamas

[nukappa]

Hi @EugeneEA,

I cannot reproduce the second error. Can you post here the output of spacemake projects list that you have after doing spacemake init and having added the species?

[EugeneEA]

Hi @EugeneEA,

Thank you for using spacemake! Can you confirm that your spacemake version is 0.7?

I think something got broken when upgrading from 0.5.5 to 0.7.

I would suggest you install the former with pip install spacemake==0.5.5 and try these commands again.

Let me know if it works.

Best, Tamas

Thanks, I've uninstalled version 0.7 repeat everything with version 0.5.5 and it works out.

[marvin-jens]

Hi @EugeneEA,

I think I've fixed the issue with a recent commit to master. Will be included in 0.7.3.