Rscript in docker image

[khoa-yelo]

Hi,

Could Rscript also be added to the container?

Error: Rscript must be installed to run splash with --supervised_test_samplesheet

[marekkokot]

Hi, just to be sure, are you using the newest version?
Can you show the full line so I can reproduce it and hopefully fix.

Best
Marek

[khoa-yelo]

singularity run splash_2.11.6.sif
Apptainer> R
bash: R: command not found
Apptainer> Rscript
bash: Rscript: command not found
Apptainer>

singularity run splash_2.11.6.sif splash input.
txt --supervised_test_samplesheet labels.txt
Welcome to SPLASH
Version:  2.11.6
Current time: 2025-12-03 23:34:28
----------------  Configuration  ---------------
input_file: input.txt
outname_prefix: result
anchor_len: 31
gap_len: 0
target_len: 31
anchor_list:
pvals_correction_col_name: pval_opt
technology: base
without_compactors: False
compactors_config:
lookup_table_config:
poly_ACGT_len: 8
artifacts:
dont_filter_illumina_adapters: False
anchor_unique_targets_threshold: 1
anchor_count_threshold: 50
anchor_samples_threshold: 1
anchor_sample_counts_threshold: 5
n_most_freq_targets_for_stats: 0
n_most_freq_targets_for_dump: 0
fdr_threshold: 0.05
min_hamming_threshold: 0
keep_top_n_target_entropy: 10000
keep_top_n_effect_size_bin: 20000
keep_significant_anchors_satc: False
keep_top_target_entropy_anchors_satc: False
keep_top_effect_size_bin_anchors_satc: False
dump_Cjs: False
max_pval_opt_for_Cjs: 0.1
n_most_freq_targets: 10
with_effect_size_cts: False
with_pval_asymp_opt: False
without_seqence_entropy: False
sample_name_to_id: sample_name_to_id.mapping.txt
dump_sample_anchor_target_count_txt: False
dump_sample_anchor_target_count_binary: False
satc_merge_dump_format: splash
supervised_test_samplesheet: labels.txt
supervised_test_anchor_sample_fraction_cutoff: 0.4
supervised_test_num_anchors: 20000
opt_num_inits: 10
opt_num_iters: 50
num_rand_cf: 50
num_splits: 1
opt_train_fraction: 0.25
without_alt_max: False
without_sample_spectral_sum: False
compute_also_old_base_pvals: False
Cjs_samplesheet:
bin_path: bin
tmp_dir:
n_threads_stage_1: 0
n_threads_stage_1_internal: 0
n_threads_stage_1_internal_boost: 1
n_threads_stage_2: 0
n_bins: 128
kmc_use_RAM_only_mode: False
kmc_max_mem_GB: 12
dont_clean_up: False
logs_dir: logs
cbc_len: 16
umi_len: 12
soft_cbc_umi_len_limit: 0
cbc_filtering_thr: 0
cell_type_samplesheet:
export_cbc_logs: False
predefined_cbc:
export_filtered_input: False
allow_strange_cbc_umi_reads: False
postprocessing_item: []
exclude_postprocessing_item: None
REMOVE_INPUT: False
------------------------------------------------
Warning: --supervised_test_samplesheet forces --dump_sample_anchor_target_count_binary
Error: Rscript must be installed to run splash with --supervised_test_samplesheet

[marekkokot]

Hi, thanks

could you try newest version, i.e. 2.11.9, because I think I have fixed this R issue in the newest version. Let me know if it helps.